1YEW | pdb_00001yew

Crystal structure of particulate methane monooxygenase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	PEG 8000, zinc acetate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.4	70

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 264.14	α = 90
b = 264.14	β = 90
c = 150.005	γ = 90

Symmetry
Space Group	P 42 21 2

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	MARRESEARCH		2003-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.377, 1.280	APS	5ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	30	91.1	0.095	7.7	3.4	118268	118268	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.874			0.612

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	SAD	THROUGHOUT	2.801	29.55	112261	5932	91.2	0.27303	0.27153	0.3	0.30157	0.31	RANDOM	69.985

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]
1.34			1.34		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.14
r_dihedral_angle_3_deg	23.693
r_dihedral_angle_4_deg	18.17
r_dihedral_angle_1_deg	10.165
r_angle_refined_deg	2.074
r_scangle_it	1.659
r_scbond_it	1.064
r_mcangle_it	0.652
r_symmetry_vdw_refined	0.585
r_mcbond_it	0.391

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.14
r_dihedral_angle_3_deg	23.693
r_dihedral_angle_4_deg	18.17
r_dihedral_angle_1_deg	10.165
r_angle_refined_deg	2.074
r_scangle_it	1.659
r_scbond_it	1.064
r_mcangle_it	0.652
r_symmetry_vdw_refined	0.585
r_mcbond_it	0.391
r_nbtor_refined	0.343
r_symmetry_hbond_refined	0.299
r_nbd_refined	0.285
r_metal_ion_refined	0.25
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.165
r_bond_refined_d	0.02
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19755
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SOLVE	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.