3LB3 | pdb_00003lb3

Two-site competitive inhibition in dehaloperoxidase-hemoglobin

X-RAY DIFFRACTION

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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
2.16	43.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.201	α = 90
b = 67.21	β = 90
c = 68.724	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 225 mm CCD		2008-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

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	1.85	35	94.2	0.101	7.95	3.4	22277	21082		2	16.4

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)
	1.85	1.9	92.9		0.322	3.35	3.4	1573

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	1.85	35	2	22277	21082	1195	94.2	0.19	0.187	0.19	0.243	0.24	RANDOM	19.54

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]
0.77			-0.57		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.351
r_dihedral_angle_4_deg	19.339
r_dihedral_angle_3_deg	16.089
r_dihedral_angle_1_deg	4.095
r_sphericity_free	2.859
r_rigid_bond_restr	2.297
r_scbond_it	2.104
r_scangle_it	2.072
r_sphericity_bonded	1.342
r_angle_refined_deg	1.157
r_mcangle_it	0.855
r_mcbond_it	0.54
r_nbtor_refined	0.3
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	117

Software

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