3O61 | pdb_00003o61

Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O52	PDB entry 3O52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	20-26% PEG 3350, 0.2 M Mg Cl, 0.1 M Tris HCL pH 8.5, 4mM GDP-mannose at a ratio of 1:1 protein:reservoir, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.276	α = 90
b = 55.824	β = 91.71
c = 158.121	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	ADSC QUANTUM 210		2009-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9787	NSLS	X6A

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	2.45	32.4	93	0.098	14.4	3.2		32636

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)
	2.45	2.49	59		0.165		1.8	1030

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3O52	2.45	32.4	32614	1644	92.73	0.2273	0.2239	0.22	0.2902	0.28	RANDOM	53.14

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]
-6.3		1.64	7.41		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.857
r_dihedral_angle_3_deg	18.397
r_dihedral_angle_4_deg	16.159
r_dihedral_angle_1_deg	6.714
r_scangle_it	2.627
r_scbond_it	1.697
r_angle_refined_deg	1.584
r_mcangle_it	1.052
r_mcbond_it	0.575
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.857
r_dihedral_angle_3_deg	18.397
r_dihedral_angle_4_deg	16.159
r_dihedral_angle_1_deg	6.714
r_scangle_it	2.627
r_scbond_it	1.697
r_angle_refined_deg	1.584
r_mcangle_it	1.052
r_mcbond_it	0.575
r_nbtor_refined	0.315
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.182
r_symmetry_hbond_refined	0.173
r_metal_ion_refined	0.136
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5971
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	163

Software

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

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.