5PYG | pdb_00005pyg

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 76)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.1M MES pH 6.1 -- 20% PEG20K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.72	α = 90
b = 45.41	β = 102.27
c = 83.6	γ = 90

Symmetry
Space Group	C 1 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 2M		2015-04-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

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	1.95	42.67	96.9	0.09	0.108	0.058	0.996	11.3	3.4		33337

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	97.2		0.652	0.784	0.427	0.687		3.3	2449

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	FOURIER SYNTHESIS	THROUGHOUT	4PTB	1.95	42.67	31697	1639	96.48	0.1791	0.1765	0.19	0.2285	0.24	RANDOM	37.854

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]
-1.17		0.3	-0.16		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.438
r_dihedral_angle_3_deg	13.728
r_dihedral_angle_4_deg	13.307
r_dihedral_angle_1_deg	6.468
r_mcangle_it	6.26
r_mcbond_it	4.041
r_mcbond_other	4.036
r_angle_refined_deg	1.781
r_angle_other_deg	1.06
r_chiral_restr	0.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.438
r_dihedral_angle_3_deg	13.728
r_dihedral_angle_4_deg	13.307
r_dihedral_angle_1_deg	6.468
r_mcangle_it	6.26
r_mcbond_it	4.041
r_mcbond_other	4.036
r_angle_refined_deg	1.781
r_angle_other_deg	1.06
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2925
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	25

Software

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