4Q98 | pdb_00004q98

Crystal structure of a fimbrilin (fimA) from Porphyromonas gingivalis W83 at 1.30 A resolution (PSI Community Target, Nakayama)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	30.00% polyethylene glycol 6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.398	α = 90
b = 67.641	β = 90.47
c = 65.576	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	PIXEL	DECTRIS PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2014-01-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97849	SSRL	BL11-1

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	1.3	47.082	94.6	0.044	15.19			73835		-3	12.99

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	1.3	1.37	74.5		0.436	2.2

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	1.3	47.082	73813	3704	94.61	0.1205	0.1186	0.12	0.1561	0.16	RANDOM	19.0056

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]
-0.06		-0.32	0.18		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.728
r_sphericity_free	27.225
r_dihedral_angle_4_deg	13.435
r_dihedral_angle_3_deg	10.781
r_sphericity_bonded	9.575
r_dihedral_angle_1_deg	6.651
r_rigid_bond_restr	3.084
r_mcangle_it	2.75
r_mcbond_it	2.242
r_mcbond_other	2.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.728
r_sphericity_free	27.225
r_dihedral_angle_4_deg	13.435
r_dihedral_angle_3_deg	10.781
r_sphericity_bonded	9.575
r_dihedral_angle_1_deg	6.651
r_rigid_bond_restr	3.084
r_mcangle_it	2.75
r_mcbond_it	2.242
r_mcbond_other	2.238
r_angle_refined_deg	1.44
r_angle_other_deg	0.844
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2659
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	1

Software

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