3QC3 | pdb_00003qc3

Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	0.16M magnesium acetate, 10.0% polyethylene glycol 8000, 20.0% Glycerol, 0.1M sodium cacodylate pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.665	α = 90
b = 47.665	β = 90
c = 220.774	γ = 90

Symmetry
Space Group	P 41

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)	2009-12-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97944,0.97894	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	2.2	29.127	97.6	0.095	8.35			24823		-3	30.791

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	2.2	2.28	96.4		0.651	1.6

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	2.2	29.127	24753	1263	99.57	0.1667	0.1644	0.17	0.2112	0.21	RANDOM	46.987

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]
1.76			1.76		-3.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.536
r_dihedral_angle_4_deg	18.958
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	4.298
r_scangle_it	2.849
r_scbond_it	2.018
r_angle_refined_deg	1.614
r_mcangle_it	1.108
r_angle_other_deg	1.029
r_mcbond_it	0.609

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.536
r_dihedral_angle_4_deg	18.958
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	4.298
r_scangle_it	2.849
r_scbond_it	2.018
r_angle_refined_deg	1.614
r_mcangle_it	1.108
r_angle_other_deg	1.029
r_mcbond_it	0.609
r_mcbond_other	0.176
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3399
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
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.