3B77 | pdb_00003b77

Crystal structure of a ph domain containing bacterial protein (exig_2160) from exiguobacterium sibiricum 255-15 at 2.42 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	NANODROP, 10.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.99	α = 90
b = 150.99	β = 90
c = 76.219	γ = 90

Symmetry
Space Group	P 4

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 315		2007-08-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9799, 0.9795, 1.0000	ALS	8.2.2

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	2.42	47.727	99.7	0.081	11.02	3.71		65515		-3	51.34

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	2.42	2.51	99.9		0.787	1.9	3.74

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.42	47.727	65460	3326	99.66	0.216	0.214	0.22	0.254	0.26	RANDOM	54.869

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]
-3.16			-3.16		6.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.51
r_dihedral_angle_4_deg	15.324
r_dihedral_angle_3_deg	14.383
r_dihedral_angle_1_deg	4.608
r_scangle_it	3.324
r_mcangle_it	2.631
r_scbond_it	2.33
r_mcbond_it	1.684
r_angle_refined_deg	1.498
r_angle_other_deg	0.901
r_mcbond_other	0.46
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.203
r_nbtor_refined	0.191
r_symmetry_vdw_other	0.182
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.134
r_symmetry_hbond_refined	0.108
r_nbtor_other	0.087
r_chiral_restr	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8975
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing