5PY9

PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 69)

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	55.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.69	α = 90
b = 45.37	β = 102.28
c = 83.46	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	1.73	40.78	98.3	0.075	0.09	0.048	0.997	11.5	3.4		48173

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	1.73	1.77	98.6		0.665	0.79	0.421	0.671		3.5	3537

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	4PTB	1.73	40.78	45771	2402	98.01	0.1775	0.1757	0.213	RANDOM	29.34

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]
-1.07		-0.02	0.39		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.873
r_dihedral_angle_4_deg	16.359
r_dihedral_angle_3_deg	13.162
r_dihedral_angle_1_deg	6.539
r_mcangle_it	5.272
r_mcbond_it	3.334
r_mcbond_other	3.333
r_angle_refined_deg	1.871
r_angle_other_deg	1.098
r_chiral_restr	0.136

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.873
r_dihedral_angle_4_deg	16.359
r_dihedral_angle_3_deg	13.162
r_dihedral_angle_1_deg	6.539
r_mcangle_it	5.272
r_mcbond_it	3.334
r_mcbond_other	3.333
r_angle_refined_deg	1.871
r_angle_other_deg	1.098
r_chiral_restr	0.136
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
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 National Science Foundation (DBI-1832184), 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 R01GM133198.