3CU2 | pdb_00003cu2

Crystal structure of ribulose-5-phosphate 3-epimerase (YP_718263.1) from Haemophilus somnus 129PT at 1.91 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.17	277	NANODROP, 16.0% PEG 8000, 0.167M Calcium acetate, 0.1M MES pH 6.17, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.01	α = 90
b = 85.01	β = 90
c = 140.16	γ = 120

Symmetry
Space Group	P 31 2 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)	2008-02-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97922, 0.97840	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	1.91	28.916	99.8	0.12	7.72			46203		-3	19.326

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	1.91	1.98	99.8		0.764	1.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.91	28.916	46156	2335	99.83	0.168	0.166	0.17	0.205	0.21	RANDOM	17.224

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]
0.46	0.23		0.46		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.868
r_dihedral_angle_3_deg	11.59
r_dihedral_angle_4_deg	10.886
r_scangle_it	7.008
r_dihedral_angle_1_deg	5.515
r_scbond_it	4.969
r_mcangle_it	3.288
r_mcbond_it	2.032
r_angle_refined_deg	1.611
r_angle_other_deg	1.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.868
r_dihedral_angle_3_deg	11.59
r_dihedral_angle_4_deg	10.886
r_scangle_it	7.008
r_dihedral_angle_1_deg	5.515
r_scbond_it	4.969
r_mcangle_it	3.288
r_mcbond_it	2.032
r_angle_refined_deg	1.611
r_angle_other_deg	1.101
r_mcbond_other	0.583
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3693
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	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.