2QFN | pdb_00002qfn

X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms of the Recombinant Heme Dehaloperoxidase Cloned from Amphitrite ornata

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	26-32% PEG 4000, 0.2M ammonium sulfate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.938	α = 90
b = 67.091	β = 90
c = 68.402	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	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic optics		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	1.62	35	99.8	0.058	14.8	5.7		34478	2	2

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)
	1.62	1.68	99.5		0.553		5.4	3388

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.62	35	2	34585	34429	1738	99.63	0.173	0.173	0.17	0.18	0.224	0.22	RANDOM	17.372

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]
-0.18			0.04		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.045
r_dihedral_angle_4_deg	15.295
r_dihedral_angle_3_deg	14.538
r_dihedral_angle_1_deg	4.311
r_scangle_it	3.733
r_scbond_it	2.647
r_mcangle_it	1.618
r_angle_refined_deg	1.162
r_mcbond_it	1.055
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.045
r_dihedral_angle_4_deg	15.295
r_dihedral_angle_3_deg	14.538
r_dihedral_angle_1_deg	4.311
r_scangle_it	3.733
r_scbond_it	2.647
r_mcangle_it	1.618
r_angle_refined_deg	1.162
r_mcbond_it	1.055
r_nbtor_refined	0.299
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2414
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	107

Software

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