2ZZ5 | pdb_00002zz5

Orotidine Monophosphate Deacarboxylase D70A/K72A double mutant from M. thermoautotrophicum complexed with 6- cyano-UMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E6Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	1.2-1.36M Sodium Citrate, 5% dioxiane, pH 6.0-8.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.556	α = 90
b = 64.359	β = 115.52
c = 61.539	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 315	default	2006-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.56	100	83.9	0.083	9.9	3.6		50081

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.59	30.2		0.43	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2E6Y	1.56	55.56	47506	2544	83.87	0.16118	0.15976	0.16	0.18679	0.19	RANDOM	18.72

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]
-1.21		-1.05	0.22		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.8
r_dihedral_angle_4_deg	17.485
r_dihedral_angle_3_deg	14.492
r_dihedral_angle_1_deg	6.033
r_scangle_it	5.372
r_scbond_it	3.321
r_mcangle_it	1.855
r_angle_refined_deg	1.793
r_mcbond_it	1.258
r_nbtor_refined	0.311
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.171
r_chiral_restr	0.128
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.114
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3220
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing