1M1P | pdb_00001m1p

P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Identical protein in P212121 spacegroup

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	ammonium sulphate, bicine, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.69	α = 90
b = 34.005	β = 110.49
c = 108.313	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 4		2000-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID13	0.9	ESRF	ID13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.55	15	92.1			91758	84418

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.55	1.59	90

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 (All)	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	Identical protein in P212121 spacegroup	1.55	14.92	91750	84418	4456		0.17458	0.1745	0.17265	0.17	0.21148	0.23	RANDOM	20.014

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]
0.13		-0.44	-0.12		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.398
r_dihedral_angle_1_deg	6.08
r_scangle_it	3.297
r_scbond_it	2.239
r_angle_refined_deg	1.573
r_mcangle_it	1.567
r_mcbond_it	0.889
r_nbd_refined	0.357
r_symmetry_vdw_refined	0.333
r_symmetry_hbond_refined	0.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.398
r_dihedral_angle_1_deg	6.08
r_scangle_it	3.297
r_scbond_it	2.239
r_angle_refined_deg	1.573
r_mcangle_it	1.567
r_mcbond_it	0.889
r_nbd_refined	0.357
r_symmetry_vdw_refined	0.333
r_symmetry_hbond_refined	0.174
r_chiral_restr	0.108
r_xyhbond_nbd_refined	0.108
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3750
Nucleic Acid Atoms
Solvent Atoms	1161
Heterogen Atoms	1052

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.