5SDS | pdb_00005sds

PanDDA analysis group deposition of ground-state model of Porphyromonas gingivalis DPP11

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	293	Morpheus Buffer system 1, 0.06M Divalents, 30% v/v Precipitant Mix 3

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.773	α = 90
b = 117.328	β = 90
c = 147.556	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	PIXEL	DECTRIS PILATUS 2M		2019-08-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91589	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.907	91.835	96.2	0.072	0.028	0.999	15.6	6.6		101212

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.907	2.074	80.8		1.094	0.445	0.67		5.7	5061

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5JWF	1.91	91.835	96027	5185	73.43	0.2148	0.2131	0.2474	RANDOM	37.635

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]
0.05			-0.04		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.322
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	16.705
r_dihedral_angle_1_deg	7.244
r_mcangle_it	4.163
r_mcbond_it	2.936
r_mcbond_other	2.936
r_angle_refined_deg	1.558
r_angle_other_deg	1.365
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.322
r_dihedral_angle_4_deg	19.029
r_dihedral_angle_3_deg	16.705
r_dihedral_angle_1_deg	7.244
r_mcangle_it	4.163
r_mcbond_it	2.936
r_mcbond_other	2.936
r_angle_refined_deg	1.558
r_angle_other_deg	1.365
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10951
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.