2GT4 | pdb_00002gt4

Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex with GDP-mannose and MG+2

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	5mM GDP-mannose 5mM glucose 5mM GDP-mannose 5mM glucose 100 mM Tris HCL p8.5 20% PEG 4000, 0.2 Mg Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.785	α = 90
b = 93.893	β = 91.23
c = 66.103	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		CCD	ADSC QUANTUM 315		2004-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

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	2.3	50	97.6	0.072	14.3	3		36595

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)
	2.3	2.38	99.9		0.406		3	3717

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RYA	2.3	77.61	111382	36594	1883	97.55	0.188	0.188	0.186	0.226	RANDOM	40.589

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]
0.99		-0.49	-3.06		2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.544
r_dihedral_angle_4_deg	17.683
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	5.917
r_scangle_it	2.469
r_scbond_it	1.655
r_angle_refined_deg	1.223
r_mcangle_it	1.172
r_mcbond_it	0.688
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.544
r_dihedral_angle_4_deg	17.683
r_dihedral_angle_3_deg	15.345
r_dihedral_angle_1_deg	5.917
r_scangle_it	2.469
r_scbond_it	1.655
r_angle_refined_deg	1.223
r_mcangle_it	1.172
r_mcbond_it	0.688
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.198
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3906
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	142

Software

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