4U28

Crystal structure of apo Phosphoribosyl isomerase A from Streptomyces sviceus ATCC 29083

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	289	1.8M Na/K phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.111	α = 90
b = 69.111	β = 90
c = 175.036	γ = 120

Symmetry
Space Group	P 65 2 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 315r		2013-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97927	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.33	50	99	0.071	10.9	9.1	60963	57655		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.35	97.9		0.834	1.82	6.7	2755

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.33	26.63	55033	2793	94.71	0.1283	0.1271	0.151	RANDOM	16.247

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		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.974
r_sphericity_free	30.031
r_dihedral_angle_4_deg	16.43
r_dihedral_angle_3_deg	11.768
r_sphericity_bonded	8.221
r_dihedral_angle_1_deg	6.136
r_mcangle_it	1.551
r_mcbond_it	1.305
r_angle_refined_deg	1.247
r_mcbond_other	1.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.974
r_sphericity_free	30.031
r_dihedral_angle_4_deg	16.43
r_dihedral_angle_3_deg	11.768
r_sphericity_bonded	8.221
r_dihedral_angle_1_deg	6.136
r_mcangle_it	1.551
r_mcbond_it	1.305
r_angle_refined_deg	1.247
r_mcbond_other	1.238
r_rigid_bond_restr	1.166
r_angle_other_deg	0.747
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1716
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.