4CVJ

Neutron Structure of Compound I intermediate of Cytochrome c Peroxidase - Deuterium exchanged 100 K

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.19	α = 90
b = 75.83	β = 90
c = 107.59	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 SATURN 944+	OSMIC HF	2013-08-01	M	SINGLE WAVELENGTH
2	1	neutron	100	IMAGE PLATE	FRM II	OSMIC HF	2013-08-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	NUCLEAR REACTOR	FRM II BEAMLINE BIODIFF	3.39	FRM II	BIODIFF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	2.18	50	99.3	0.074						16.5	4.7		22053
2	2.3	50	90.7	0.173						4.6	2.3		13661

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.25		0.428						5.9	1.7
2	2.5	2.59		0.428						1.5	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.182	17.057		1.38		22053	1104	98.38		0.1516	0.1488	0.2052
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.501	46.225		1.34		13661	683	90.67		0.1914	0.1873	0.272

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]
0.0213			2.2575		-3.5349
-1.9296			6.9359		-5.0063

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.757
f_angle_d	1.261
f_chiral_restr	0.091
f_bond_d	0.011
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2356
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.