3VRC | pdb_00003vrc

Crystal structure of cytochrome c' from Thermochromatium tepidum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BBH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	30% PEG 400, 0.1M cadmium chloride, 0.1M sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.31	α = 90
b = 57.189	β = 94.81
c = 54.225	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210	mirrors	2007-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.8	Photon Factory	AR-NW12A

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	50	94.3	0.04	42.6	3.4		127655

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	1.02	70.2		0.21	2.6	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1BBH	1	50	127619	121269	6350	94.2	0.1304	0.1292	0.1303	0.1534	0.1551	RANDOM	16.6008

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]
-0.66		-0.2	1.32		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.809
r_sphericity_free	21.72
r_dihedral_angle_4_deg	15.903
r_dihedral_angle_3_deg	13.226
r_sphericity_bonded	11.907
r_rigid_bond_restr	6.752
r_dihedral_angle_1_deg	4.799
r_angle_refined_deg	2.482
r_chiral_restr	0.106
r_gen_planes_refined	0.027
r_bond_refined_d	0.021

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1893
Nucleic Acid Atoms
Solvent Atoms	479
Heterogen Atoms	116

Software

Software
Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling