3ORD | pdb_00003ord

Structural Evidence for Stabilization of Inhibitor Binding by a Protein Cavity in the Dehaloperoxidase-Hemoglobin from Amphitrite ornata

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QFK	PDB ENTRY 2qfk

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	0.2 M ammonium sulfate, 32% PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.674	α = 90
b = 67.805	β = 90
c = 68.304	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	RIGAKU SATURN 92		2009-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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	2.22	48.121	93.24	0.132	16.8	10.7	13324	12423		2	22.8

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	2.22	2.278	83.61		0.571	3.3	8.2	974

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2qfk	2.22	30.5	2	13323	12423	635	93.24	0.21563	0.21203	0.21	0.2889	0.28	RANDOM	22.841

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]
1.63			-1.15		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.338
r_dihedral_angle_4_deg	22.484
r_dihedral_angle_3_deg	18.26
r_dihedral_angle_1_deg	5.464
r_scangle_it	2.833
r_scbond_it	1.817
r_angle_refined_deg	1.375
r_mcangle_it	1.078
r_mcbond_it	0.601
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.338
r_dihedral_angle_4_deg	22.484
r_dihedral_angle_3_deg	18.26
r_dihedral_angle_1_deg	5.464
r_scangle_it	2.833
r_scbond_it	1.817
r_angle_refined_deg	1.375
r_mcangle_it	1.078
r_mcbond_it	0.601
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	100

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
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.