4WMH | pdb_00004wmh

Structure of heme oxygenase-2 containing residues 1-288 lacking the membrane spanning region

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QPP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	20% PEG 1.5K and 100mM BTP pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.69	α = 90
b = 35.69	β = 90
c = 366.706	γ = 90

Symmetry
Space Group	P 43 2 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	MARMOSAIC 300 mm CCD		2007-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97857	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	91.68	99.82	17.36	25.3		8270

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	2QPP	2.5	91.68	8270	936	99.82	0.2308	0.2261	0.24	0.2699	0.28	RANDOM	52.899

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]
1.74			1.74		-3.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.284
r_dihedral_angle_4_deg	19.34
r_dihedral_angle_3_deg	14.33
r_dihedral_angle_1_deg	4.975
r_mcangle_it	2.399
r_mcbond_it	1.475
r_mcbond_other	1.475
r_angle_refined_deg	0.947
r_angle_other_deg	0.73
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.284
r_dihedral_angle_4_deg	19.34
r_dihedral_angle_3_deg	14.33
r_dihedral_angle_1_deg	4.975
r_mcangle_it	2.399
r_mcbond_it	1.475
r_mcbond_other	1.475
r_angle_refined_deg	0.947
r_angle_other_deg	0.73
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1708
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	1

Software

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

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.