5Q99 | pdb_00005q99

PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 255)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	30% PEG 1000, 0.1M MIB buffer

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.709	α = 90
b = 57.132	β = 90
c = 115.063	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		PIXEL	DECTRIS PILATUS 6M		2017-04-12		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	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	1.31	57.12	100	0.055	0.06	0.024	0.999	11.5	5.9		82720

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	1.31	1.34	99.9		1.179	1.358	0.665	0.523		4.1	6004

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	5aho	1.31	57.12	77794	3987	98.89	0.2007	0.1993	0.2	0.2268	0.23	RANDOM	25.331

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]
-0.1			0.68		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.864
r_dihedral_angle_4_deg	20.284
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	6.553
r_mcangle_it	4.556
r_mcbond_it	2.933
r_mcbond_other	2.929
r_angle_refined_deg	2.182
r_angle_other_deg	1.133
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.864
r_dihedral_angle_4_deg	20.284
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	6.553
r_mcangle_it	4.556
r_mcbond_it	2.933
r_mcbond_other	2.929
r_angle_refined_deg	2.182
r_angle_other_deg	1.133
r_chiral_restr	0.132
r_bond_refined_d	0.026
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2692
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	8

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.