7O6W | pdb_00007o6w

Crystal structure of (the) VEL1 VEL polymerising domain (I664D mutant)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.25M (NH4)H2PO4

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.259	α = 90
b = 79.259	β = 90
c = 59.957	γ = 120

Symmetry
Space Group	P 63

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 PILATUS3 6M		2020-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.979500	Diamond	I24

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	2.64	27.49	98.8	0.068	0.069	0.011	1	37	20		6333

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	2.64	2.77	92		1.045	1	0.183	0.842		15

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.64	27.49	5671	631	98.64	0.21527	0.21157	0.22	0.24916	0.22	RANDOM	89.726

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]
-1.43	-0.72		-1.43		4.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.308
r_dihedral_angle_4_deg	17.466
r_dihedral_angle_3_deg	15.326
r_long_range_B_refined	5.875
r_long_range_B_other	5.873
r_dihedral_angle_1_deg	4.332
r_scangle_other	1.314
r_mcangle_other	1.256
r_mcangle_it	1.255
r_angle_refined_deg	1.012
r_angle_other_deg	1.008
r_scbond_it	0.777
r_scbond_other	0.777
r_mcbond_it	0.756
r_mcbond_other	0.751
r_chiral_restr	0.053
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1140
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
CRANK2	phasing
Coot	model building
PDB_EXTRACT	data extraction