4JM8

Crystal structure of Cytochrome C Peroxidase W191G-Gateless in complex with 2,6-diaminopyridine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	283	Apo crystal grown in 500mM MES, pH 6.0. Soaked into 50mM 2,6-diaminopyridine, 25% MPD pH 4.5 (30min-1h), vapor diffusion, sitting drop, temperature 283K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.843	α = 90
b = 74.519	β = 90
c = 106.464	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	80	CCD	ADSC QUANTUM 315r		2009-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	61.08					98290

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	30.05	98290	4924	98.26	0.118	0.117	0.1368	RANDOM	20.4693

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]
0.57			0.75		-1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.596
r_dihedral_angle_4_deg	26.574
r_dihedral_angle_3_deg	13.591
r_dihedral_angle_1_deg	5.974
r_scangle_it	5.317
r_scbond_it	3.933
r_mcangle_it	2.711
r_mcbond_it	1.871
r_rigid_bond_restr	1.73
r_angle_refined_deg	1.691

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.596
r_dihedral_angle_4_deg	26.574
r_dihedral_angle_3_deg	13.591
r_dihedral_angle_1_deg	5.974
r_scangle_it	5.317
r_scbond_it	3.933
r_mcangle_it	2.711
r_mcbond_it	1.871
r_rigid_bond_restr	1.73
r_angle_refined_deg	1.691
r_angle_other_deg	1.013
r_mcbond_other	0.704
r_chiral_restr	0.111
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2328
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.