5S9E | pdb_00005s9e

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
1.71	28.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.069	α = 90
b = 27.088	β = 100.38
c = 55.915	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		2020-09-16		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9127	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	1.18	39.87	74.3	0.055	0.066	0.037	0.996	9.3	2.6		29598

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	1.18	1.24	59.7		0.404	0.554	0.377	0.83		1.2	3375

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	1.18	39.9	28131	1466	74.12	0.175	0.1737	0.23	0.2008	0.26	RANDOM	15.027

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]
0.08		0.43	0.63		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.952
r_dihedral_angle_4_deg	14.903
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	5.21
r_angle_refined_deg	1.623
r_angle_other_deg	1.552
r_mcangle_it	1.51
r_mcbond_other	0.886
r_mcbond_it	0.877
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.952
r_dihedral_angle_4_deg	14.903
r_dihedral_angle_3_deg	13.29
r_dihedral_angle_1_deg	5.21
r_angle_refined_deg	1.623
r_angle_other_deg	1.552
r_mcangle_it	1.51
r_mcbond_other	0.886
r_mcbond_it	0.877
r_chiral_restr	0.098
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	24

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.