2B7R | pdb_00002b7r

Structure of E378D mutant flavocytochrome c3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	0.1M TrisHCl, 80mM NaCl, 10mM Na fumarate, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.961	α = 90
b = 92.879	β = 91.17
c = 79.486	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	IMAGE PLATE	MARRESEARCH		2001-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.87	EMBL/DESY, HAMBURG	BW7B

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	1.7	20	98.4	0.067	18.7		73408	72178			18.3

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)
	1.7	1.76	94.6		0.129	6.9		6862

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	1QJD	1.7	20	68525	3629	98.21	0.15768	0.15646	0.1553	0.18034	0.1789	RANDOM	18.322

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]
0.71		-0.16	0.4		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.491
r_dihedral_angle_4_deg	17.873
r_dihedral_angle_3_deg	11.902
r_dihedral_angle_1_deg	5.579
r_scangle_it	2.742
r_scbond_it	1.772
r_angle_refined_deg	1.314
r_mcangle_it	1.009
r_mcbond_it	0.561
r_nbtor_refined	0.283
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.118
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.111
r_metal_ion_refined	0.035
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4176
Nucleic Acid Atoms
Solvent Atoms	1084
Heterogen Atoms	234

Software

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