6VLB | pdb_00006vlb

Crystal structure of ligand-free UDP-GlcNAc 2-epimerase from Neisseria meningitidis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F6D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	50% (v/v) PEG-200, 100 mM phosphate-citrate, pH 4.2, and 200 mM NaCl.

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.55	α = 90
b = 49.51	β = 90.93
c = 81.22	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 315r		2013-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12709	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.85	40	98.7	0.065	0.077	0.997	10.8	3.46		71340		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	97		0.427	0.498	0.89	2.65	3.75

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1F6D	1.85	36.42	67746	3593	98.67	0.1841	0.1824	0.2157	RANDOM	34.714

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]
-1.2		-0.14	2.27		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.501
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_4_deg	9.815
r_dihedral_angle_1_deg	6.177
r_angle_refined_deg	1.466
r_angle_other_deg	1.436
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.501
r_dihedral_angle_3_deg	12.238
r_dihedral_angle_4_deg	9.815
r_dihedral_angle_1_deg	6.177
r_angle_refined_deg	1.466
r_angle_other_deg	1.436
r_chiral_restr	0.075
r_bond_refined_d	0.01
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	5863
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.