5R65 | pdb_00005r65

PanDDA analysis group deposition -- Crystal Structure of HUMAN CLEAVAGE FACTOR IM in complex with FMOPL000387a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	277	0.1M acetate pH 5.1, 0.0025M ZnAC, 6% PEG3K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.63	α = 90
b = 59.63	β = 90
c = 215.04	γ = 120

Symmetry
Space Group	P 32 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		2017-07-08		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	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	2.28	107.52	99.5	0.218	0.232	0.076	0.996	9.2	9.2		21066

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	2.28	2.34	95.1		9.819	10.471	3.571	0.506		8.6	1446

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	3BAP	2.28	71.78	19948	1054	99.29	0.2121	0.2085	0.23	0.2786	0.29	RANDOM	40.464

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]
-0.21	-0.1		-0.21		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.598
r_dihedral_angle_4_deg	19.328
r_dihedral_angle_3_deg	15.166
r_dihedral_angle_1_deg	8.068
r_mcangle_it	5.314
r_mcbond_other	3.47
r_mcbond_it	3.468
r_angle_refined_deg	1.615
r_angle_other_deg	1.208
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.598
r_dihedral_angle_4_deg	19.328
r_dihedral_angle_3_deg	15.166
r_dihedral_angle_1_deg	8.068
r_mcangle_it	5.314
r_mcbond_other	3.47
r_mcbond_it	3.468
r_angle_refined_deg	1.615
r_angle_other_deg	1.208
r_chiral_restr	0.076
r_bond_refined_d	0.008
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	3160
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	46

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.