2QPP | pdb_00002qpp

Crystal structure of human heme oxygenase-2 C127A (HO-2) with bound heme

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q32	PDB entry 2Q32

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein solution (5 mg/ml Protein, 1:1 ratio HEME, 2% DMSO, 0.050 M Potassium chloride, 0.050 M Tris-HCl pH 7.5) mixed in a 1.5:1 ratio with the Well solution (33% PEG DME 500, 0.020 M Magnesium chloride, 0.10 M HEPES pH 7.5). Cryoprotected with well solution, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.977	α = 90
b = 85.094	β = 90
c = 97.846	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 300 mm CCD	Adjustable focus K-B pair Si plus Pt, Rh coatings	2007-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97946	APS	23-ID-B

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	2.32	42.413	85.6	0.083	16.268	11.6		24030

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)
1	2.32	2.4	27.4		0.715	0.776	1.8	752

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 2Q32	2.61	40.962	19515	1005	99.364	0.205	0.202	0.2	0.256	0.25	RANDOM	65.958

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]
-0.34			-1.216		1.555

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.971
r_dihedral_angle_4_deg	19.242
r_dihedral_angle_3_deg	15.542
r_dihedral_angle_1_deg	4.47
r_mcangle_it	1.234
r_scangle_it	1.167
r_angle_refined_deg	0.951
r_scbond_it	0.859
r_mcbond_it	0.732
r_nbtor_refined	0.29
r_symmetry_hbond_refined	0.266
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3552
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	86

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling