2YCG | pdb_00002ycg

Structure of unreduced ferric cytochrome c peroxidase obtained by multicrystal method

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XIL	PDB ENTRY 2XIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.118	α = 90
b = 75.6	β = 90
c = 106.752	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	RIGAKU-MSC SATURN 944+	VARIMAX HF OPTICS (75 MICROMETER FOCUS, 1.2KW)	2010-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	1.81	12.38	92.24	0.056	16.9	4		35815

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	1.81	1.9	87.7		0.099	9.6	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ENTRY 2XIL	1.81	10	33851		88	0.1512		0.14	0.1963	0.18	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
2		3010

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.2
s_similar_adp_cmpnt	0.056
s_non_zero_chiral_vol	0.049
s_zero_chiral_vol	0.048
s_bond_d	0.045
s_angle_d	0.029
s_from_restr_planes	0.0261
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	64

Software

Software
Software Name	Purpose
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

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.