7NSS | pdb_00007nss

Bdellovibrio bacteriovorus PGI in P3121 spacegroup

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B0Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	0.2 M ammonium acetate, 0.1 M sodium acetate pH 5.0 and 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.03	α = 90
b = 101.03	β = 90
c = 76.7	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	DECTRIS PILATUS 6M-F		2016-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.84	57.74	95.8	0.101	0.106	0.034	1	23.2	18.7		37920			28.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.87			1.919	0.821	0.559	1.3

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	1b0z	1.84	57.74	36033	1859	95.82	0.1908	0.1892	0.1932	0.2206	0.2209	RANDOM	35.017

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]
0.67	0.33		0.67		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.03
r_dihedral_angle_3_deg	15.524
r_dihedral_angle_4_deg	14.661
r_dihedral_angle_1_deg	6.91
r_angle_other_deg	2.273
r_angle_refined_deg	1.476
r_chiral_restr	0.073
r_bond_other_d	0.035
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3180
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHENIX	phasing