8BW3 | pdb_00008bw3

PanDDA analysis -- 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	7AV9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277.5	20% PEG 8000, 0.04M POTASSIUM PHOSPHATE

Crystal Properties
Matthews coefficient	Solvent content
1.7	27.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.957	α = 90
b = 26.805	β = 99.662
c = 55.183	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		2020-10-08	M	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)	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	1.3	54.4	96.7	0.996	9.1	2.9		28411

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	87.3		0.417	0.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AV9	1.3	54.4	28384	1420	96.132	0.209	0.2074	0.22	0.2422	0.25	21.35

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		0.18	0.434		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.65
r_dihedral_angle_6_deg	15.3
r_dihedral_angle_2_deg	12.831
r_scangle_it	7.729
r_scangle_other	7.724
r_lrange_it	7.272
r_lrange_other	6.956
r_rigid_bond_restr	6.886
r_scbond_it	6.162
r_scbond_other	6.157
r_dihedral_angle_1_deg	5.717
r_mcangle_other	4.244
r_mcangle_it	4.236
r_mcbond_it	3.552
r_mcbond_other	3.549
r_angle_refined_deg	1.445
r_angle_other_deg	0.565
r_nbd_refined	0.242
r_symmetry_nbd_refined	0.215
r_nbd_other	0.211
r_xyhbond_nbd_refined	0.203
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.177
r_chiral_restr	0.076
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	990
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing