3I83 | pdb_00003i83

Crystal structure of 2-dehydropantoate 2-reductase from Methylococcus capsulatus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.7	294	100mM sodium acetate pH 4.7, 16% PEG 4K, 100mM ammonium acetate, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.851	α = 90
b = 79.179	β = 90
c = 100.626	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2009-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	28.605	99.5	0.098	0.098	15.6	10.7	48423	48181			22.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	99.2		0.475	0.475	4.9	10.5	6913

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	1.9	20	48396	48101	2355	99.39	0.194	0.192	0.2	0.227	0.24	RANDOM	27.306

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]
0.57			-0.07		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.816
r_dihedral_angle_4_deg	15.993
r_dihedral_angle_3_deg	14.596
r_dihedral_angle_1_deg	5.583
r_scangle_it	3.994
r_scbond_it	2.557
r_mcangle_it	1.611
r_angle_refined_deg	1.523
r_angle_other_deg	0.985
r_mcbond_it	0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.816
r_dihedral_angle_4_deg	15.993
r_dihedral_angle_3_deg	14.596
r_dihedral_angle_1_deg	5.583
r_scangle_it	3.994
r_scbond_it	2.557
r_mcangle_it	1.611
r_angle_refined_deg	1.523
r_angle_other_deg	0.985
r_mcbond_it	0.934
r_mcbond_other	0.278
r_chiral_restr	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4429
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	4

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.