3C5Y

Crystal structure of a putative ribose 5-phosphate isomerase (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	277	NANODROP, 0.2M LiNO3, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.754	α = 90
b = 109.462	β = 102.92
c = 167.569	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	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837	SSRL	BL11-1

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	1.81	49.147	96.9	0.063	8.69			330786		-3	22.954

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	1.81	1.87	97.2		0.429	2.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2PPW	1.81	49.147	330758	16707	96.93	0.173	0.17	0.22	RANDOM	25.658

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]
1.88		0.77			-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.673
r_dihedral_angle_3_deg	11.616
r_dihedral_angle_4_deg	11.224
r_scangle_it	7.71
r_scbond_it	5.503
r_dihedral_angle_1_deg	3.778
r_mcangle_it	3.186
r_mcbond_it	2.136
r_angle_refined_deg	1.709
r_angle_other_deg	1.547

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.673
r_dihedral_angle_3_deg	11.616
r_dihedral_angle_4_deg	11.224
r_scangle_it	7.71
r_scbond_it	5.503
r_dihedral_angle_1_deg	3.778
r_mcangle_it	3.186
r_mcbond_it	2.136
r_angle_refined_deg	1.709
r_angle_other_deg	1.547
r_mcbond_other	0.643
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25574
Nucleic Acid Atoms
Solvent Atoms	2655
Heterogen Atoms	276

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
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 R01GM133198.