2OC9 | pdb_00002oc9

Crystal structure of human purine nucleoside phosphorylase mutant H257G with Imm-H

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RR6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.17	α = 90
b = 142.17	β = 90
c = 168.674	γ = 120

Symmetry
Space Group	H 3 2

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		2006-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.100	NSLS	X29A

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	2.59	30	97.2	0.079	0.069	9.4	6.5	20553	19978			63.8

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	2.59	2.69	75.8		0.437	0.437	1.6	2.8	1543

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	1RR6	2.59	8	19832	19238	994	97	0.197	0.197	0.194	0.2	0.243	0.24	RANDOM	56.926

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.889
r_dihedral_angle_3_deg	20.742
r_dihedral_angle_4_deg	20.706
r_dihedral_angle_1_deg	8.252
r_scangle_it	4.692
r_scbond_it	3.06
r_mcangle_it	2.286
r_angle_refined_deg	2.246
r_mcbond_it	1.34
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.889
r_dihedral_angle_3_deg	20.742
r_dihedral_angle_4_deg	20.706
r_dihedral_angle_1_deg	8.252
r_scangle_it	4.692
r_scbond_it	3.06
r_mcangle_it	2.286
r_angle_refined_deg	2.246
r_mcbond_it	1.34
r_nbtor_refined	0.324
r_nbd_refined	0.261
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.135
r_symmetry_hbond_refined	0.05
r_bond_refined_d	0.024
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2176
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	24

Software

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

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.