2PS1 | pdb_00002ps1

S. cerevisiae orotate phosphoribosyltransferase complexed with orotic acid and PRPP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRZ	PDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	288.15	38% PEG 4000, 0.14M ammonium acetate, 0.1M sodium acetate, 2.0mM magnesium chloride, 5.0mM PRPP, 5.0mM orotic acid, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.788	α = 90.59
b = 50.051	β = 105.88
c = 50.078	γ = 92.99

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.75	50	92.9	0.049	0.043	17.8	3.6	39461	36660		0.2	21.245

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	63.7		0.251	0.211	3.2	2.5	2533

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PRZ (S. cerevisiae OPRTase complexed with OMP)	1.75	49.94	39534	36660	1844	92.73	0.195	0.195	0.194	0.19	0.217	0.22	RANDOM	23.628

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.24	0.09	1.14	0.32	0.63	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.196
r_dihedral_angle_3_deg	14.733
r_dihedral_angle_4_deg	10.863
r_dihedral_angle_1_deg	4.831
r_scangle_it	1.536
r_angle_refined_deg	1.11
r_scbond_it	0.982
r_mcangle_it	0.853
r_mcbond_it	0.484
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.196
r_dihedral_angle_3_deg	14.733
r_dihedral_angle_4_deg	10.863
r_dihedral_angle_1_deg	4.831
r_scangle_it	1.536
r_angle_refined_deg	1.11
r_scbond_it	0.982
r_mcangle_it	0.853
r_mcbond_it	0.484
r_nbtor_refined	0.298
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.139
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.091
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3446
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	68

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.