7QCE | pdb_00007qce

Crystal structure of an atypical PHD finger of VIN3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.06M Morpheus Divalents, 1.1M Morpheus Buffer System pH 6.5, 10% PEG 20K, 20% PEG 500 MME

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.641	α = 90
b = 58.641	β = 90
c = 225.395	γ = 120

Symmetry
Space Group	P 31 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 EIGER2 X 16M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	50.84	100	0.135	0.997	13.3	19.6		27349

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	2.1	2.16			0.81

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	2.1	50.84	25824	1440	99.93	0.23198	0.23017	0.23	0.2645	0.27	RANDOM	58.149

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]
-1.12	-0.56		-1.12		3.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.184
r_long_range_B_other	14.578
r_long_range_B_refined	14.567
r_scangle_other	14.008
r_dihedral_angle_3_deg	12.328
r_scbond_it	12.045
r_scbond_other	12.043
r_dihedral_angle_4_deg	11.27
r_mcangle_it	7.965
r_mcangle_other	7.965
r_mcbond_other	7.668
r_mcbond_it	7.66
r_dihedral_angle_1_deg	4.994
r_angle_refined_deg	1.286
r_angle_other_deg	0.99
r_chiral_restr	0.059
r_bond_refined_d	0.005
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	2630
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	19

Software

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