5C9M

The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	20 mg/ml protein, PEG 4000, isopropanol, sodium acetate, potassium ferricyanate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.517	α = 109.86
b = 52.567	β = 92.93
c = 61.771	γ = 92.2

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD		2014-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.362	57.962	92.37	0.052	14.1	3.9	80448	76544			13

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	1.362	1.398	66.24		0.58	2.2	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5C0Z	1.362	57.96	76544	3901	92.37	0.131	0.129	0.13	0.16982	0.17	RANDOM	21.413

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]
0.04	0.04	0.89	-0.51	0.85	-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.915
r_dihedral_angle_2_deg	31.917
r_dihedral_angle_4_deg	31.575
r_sphericity_bonded	12.158
r_dihedral_angle_3_deg	12.075
r_dihedral_angle_1_deg	6.497
r_long_range_B_refined	3.725
r_long_range_B_other	3.046
r_rigid_bond_restr	2.519
r_scangle_other	2.45
r_scbond_it	2.042
r_scbond_other	2.033
r_mcangle_it	1.824
r_mcangle_other	1.824
r_angle_refined_deg	1.803
r_mcbond_it	1.482
r_mcbond_other	1.482
r_angle_other_deg	1.058
r_chiral_restr	0.122
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_gen_planes_other	0.014
r_bond_other_d	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3220
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	224

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	phasing
Aimless	data scaling
XDS	data reduction