5RVZ | pdb_00005rvz

PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1929757385

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	293	0.1M Hepes, 0.1M Magnesium chloride, 20% PEG 6K, 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.149	α = 90
b = 146.911	β = 102.9
c = 87.327	γ = 90

Symmetry
Space Group	P 1 21 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		2020-02-21		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)	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	1.989	85.122	92.4	0.188	0.097	0.99	6.9	3.7		78185

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.989	2.242	66.3		0.912	0.477	0.555		3.6

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 (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	6SY1	1.98	85.12	74266	3950	58.32	0.1688	0.1657	0.17	0.2248	0.22	RANDOM	24.78

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]
-0.23		0.19	-0.01		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.493
r_dihedral_angle_4_deg	15.808
r_dihedral_angle_3_deg	14.943
r_dihedral_angle_1_deg	7.556
r_mcangle_it	3.261
r_mcbond_it	2.018
r_mcbond_other	2.017
r_angle_refined_deg	1.529
r_angle_other_deg	1.296
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.493
r_dihedral_angle_4_deg	15.808
r_dihedral_angle_3_deg	14.943
r_dihedral_angle_1_deg	7.556
r_mcangle_it	3.261
r_mcbond_it	2.018
r_mcbond_other	2.017
r_angle_refined_deg	1.529
r_angle_other_deg	1.296
r_chiral_restr	0.066
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	13480
Nucleic Acid Atoms
Solvent Atoms	1809
Heterogen Atoms	70

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.