6TRJ | pdb_00006trj

LEDGF/p75 IBD dimer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M DL-Glutamic acid monohydrate; 0.1M DL-Alanine; 0.1M Glycine; 0.1M DL-Lysine monohydrochloride; 0.1M DL-Serine; 0.1 M Tris (base); BICINE pH 8.5; 20% v/v Glycerol; 10% w/v PEG 4000 (Morpheus Molecular Dimensions condition H11)

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.748	α = 90
b = 58.748	β = 90
c = 48.232	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 PILATUS 300K		2017-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.3	50.88	91.8	0.043	0.047	0.999	17.65	5.467		22048			21.766

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.38	66.5		0.827	1.001	0.498	0.96	2.615

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	AB INITIO PHASING	THROUGHOUT	1.3	50.88	20959	1089	91.74	0.1393	0.1373	0.14	0.1767	0.18	RANDOM	22.167

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]
0.05	0.02		0.05		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.096
r_sphericity_free	25.953
r_sphericity_bonded	13.458
r_dihedral_angle_4_deg	12.178
r_dihedral_angle_3_deg	11.584
r_rigid_bond_restr	3.951
r_dihedral_angle_1_deg	3.862
r_angle_refined_deg	1.518
r_angle_other_deg	1.098
r_chiral_restr	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	684
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Arcimboldo	phasing