2ZZS

Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	293	10mM sodium phosphate buffer (pH 7.0), 0.1M phosphate-citrate (pH 4.2), 0.2M NaCl, 20%(w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.949	α = 71.5
b = 87.612	β = 72.98
c = 103.847	γ = 83.68

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	ADSC QUANTUM 270		2008-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

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	1.8	20	94.5	0.063			235784	223962

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	77.9		0.205	0.23	14.1	2.1	19421

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GDV	1.8	20	235784	223962	11820	100	0.19519	0.19269	0.24213	RANDOM	26.068

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]
-0.26	0.48	-0.16	-0.79	0.04	1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.766
r_dihedral_angle_3_deg	14.377
r_dihedral_angle_1_deg	8.065
r_dihedral_angle_4_deg	7.43
r_scangle_it	4.072
r_scbond_it	2.77
r_angle_refined_deg	1.777
r_mcangle_it	1.742
r_mcbond_it	1.001
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.766
r_dihedral_angle_3_deg	14.377
r_dihedral_angle_1_deg	8.065
r_dihedral_angle_4_deg	7.43
r_scangle_it	4.072
r_scbond_it	2.77
r_angle_refined_deg	1.777
r_mcangle_it	1.742
r_mcbond_it	1.001
r_chiral_restr	0.111
r_bond_refined_d	0.018
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18378
Nucleic Acid Atoms
Solvent Atoms	1624
Heterogen Atoms	1400

Software

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

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.