5S8S | pdb_00005s8s

PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z198194396 synthetic derivative

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	20% PEG 8000, 0.04M POTASSIUM PHOSPHATE

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.727	α = 90
b = 27.107	β = 100.02
c = 55.917	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 6M		2019-04-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	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	1.22	55.064	82	0.053	0.029	0.998	12.2	3		21906

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	1.22	1.383	37.1		0.585	0.371	0.828		2.1	1096

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	5RJI	1.22	55.06	20812	1810	60.58	0.176	0.1739	0.23	0.2143	0.25	RANDOM	15.962

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		0.21	0.02		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.56
r_dihedral_angle_3_deg	15.009
r_dihedral_angle_4_deg	10
r_dihedral_angle_1_deg	4.979
r_mcangle_it	1.547
r_angle_refined_deg	1.528
r_angle_other_deg	1.478
r_mcbond_other	0.886
r_mcbond_it	0.88
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.56
r_dihedral_angle_3_deg	15.009
r_dihedral_angle_4_deg	10
r_dihedral_angle_1_deg	4.979
r_mcangle_it	1.547
r_angle_refined_deg	1.528
r_angle_other_deg	1.478
r_mcbond_other	0.886
r_mcbond_it	0.88
r_chiral_restr	0.081
r_bond_refined_d	0.009
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	990
Nucleic Acid Atoms
Solvent Atoms	189
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.