3KEB | pdb_00003keb

Thiol peroxidase from Chromobacterium violaceum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q98	PDB entry 1Q98

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	20% PEG-3350, 0.2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2	38.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.63	α = 90
b = 59.387	β = 98.3
c = 93.484	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315		2009-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-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	1.8	43	99	0.087	8.2	4	74165	74165			29.2

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	1.8	1.83	88.5		0.502	2.13	2.9	3250

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB entry 1Q98	1.8	43	74115	74115	3740	98.33	0.207	0.207	0.206	0.2136	0.242	0.2466	RANDOM	18.685

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]
1.75		0.53	-1.04		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.101
r_dihedral_angle_4_deg	19.539
r_dihedral_angle_3_deg	14.805
r_dihedral_angle_1_deg	6.182
r_scangle_it	4.745
r_scbond_it	3.085
r_mcangle_it	1.894
r_angle_refined_deg	1.732
r_mcbond_it	1.115
r_angle_other_deg	0.978
r_mcbond_other	0.394
r_chiral_restr	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5616
Nucleic Acid Atoms
Solvent Atoms	761
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
MOLREP	phasing
HKL-3000	phasing