3HSA | pdb_00003hsa

Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	5.0000% polyethylene glycol 3000, 22.0000% polyethylene glycol 400, 10.0000% Glycerol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.23	α = 90
b = 129.49	β = 90
c = 138.73	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-05-14	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-05-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97920	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97920,0.97934,0.91837	SSRL	BL9-2

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	1.99	47.351	98.4	0.087	10.18	3.61		41702		-3	22.653

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	1.99	2.06	99.1		0.531	2.3

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	1.99	47.351	41641	2115	98.47	0.191	0.189	0.19	0.233	0.24	RANDOM	22.491

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]
1.33			-0.51		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.871
r_dihedral_angle_4_deg	19.476
r_dihedral_angle_3_deg	13.43
r_dihedral_angle_1_deg	5.294
r_scangle_it	4.304
r_scbond_it	2.684
r_mcangle_it	2.454
r_angle_refined_deg	1.664
r_mcbond_it	1.403
r_angle_other_deg	0.981

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.871
r_dihedral_angle_4_deg	19.476
r_dihedral_angle_3_deg	13.43
r_dihedral_angle_1_deg	5.294
r_scangle_it	4.304
r_scbond_it	2.684
r_mcangle_it	2.454
r_angle_refined_deg	1.664
r_mcbond_it	1.403
r_angle_other_deg	0.981
r_mcbond_other	0.323
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4634
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	50

Software

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

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.