5S92 | pdb_00005s92

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5RJI	5RJI

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
1.72	28.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.643	α = 90
b = 26.989	β = 99.92
c = 55.818	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		2020-08-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9126	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	1.19	54.99	87.8	0.054	0.067	0.039	0.993	6.8	2.4		34124

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	1.19	1.21	40		0.959	1.356	0.959	0.504		1.1	742

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	1.19	54.98	30619	1595	82.67	0.2009	0.1995	0.2288	0.2275	0.2445	RANDOM	16.382

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]
-0.32		0.55	0.92		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.467
r_dihedral_angle_3_deg	14.381
r_dihedral_angle_4_deg	13.291
r_dihedral_angle_1_deg	5.163
r_mcangle_it	1.553
r_angle_refined_deg	1.523
r_angle_other_deg	1.495
r_mcbond_other	0.953
r_mcbond_it	0.945
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
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	21

Software

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