Experiment: 7MRI

Crystal structure of N63T yeast iso-1-cytochrome c

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YCC	PDB entry 2YCC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Tris, pH 8.5, 30% w/v PEG1000

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.25	α = 90
b = 59.25	β = 90
c = 92.3	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2019-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.9795	SSRL	BL12-2

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	2.46	41.93	99.73	0.19	6.5	6.4		11569

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	2.46	2.52			0.73

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	PDB entry 2YCC	2.46	41.93	11022	547	99.71	0.1675	0.1662	0.1661	0.208	0.2191	RANDOM	33.069

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]
1.62			1.62		-3.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.448
r_dihedral_angle_4_deg	27.111
r_dihedral_angle_3_deg	18.92
r_dihedral_angle_1_deg	6.807
r_angle_refined_deg	1.628
r_chiral_restr	0.119
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2517
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing