3LB2 | pdb_00003lb2

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
2.18	43.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.007	α = 90
b = 67.358	β = 90
c = 69.42	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		2007-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.91942	APS	22-ID

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	1.06	35	98.7	0.052	22.5	4	121970	115854		2	6.8

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)
	1.06	1.09	93.8		0.318	3.8	3.3	8490

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	1.06	35	2	121970	115854	6116	98.7	0.169	0.168	0.18	0.183	0.19	RANDOM	10.17

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]
0.02			-0.1		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.01
r_dihedral_angle_4_deg	15.961
r_dihedral_angle_3_deg	14.42
r_dihedral_angle_1_deg	3.973
r_sphericity_free	2.377
r_scangle_it	1.898
r_sphericity_bonded	1.618
r_scbond_it	1.352
r_angle_refined_deg	1.17
r_mcangle_it	1.074
r_rigid_bond_restr	0.74
r_mcbond_it	0.663
r_nbtor_refined	0.308
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.178
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.088
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	112

Software

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