4OCT | pdb_00004oct

Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O61	related to pdb entry 4O61

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.005 M of each manganous sulfate and 2-oxyglutarate were added to the protein stock solution. Reservoir: 20% PEG-3350, 0.2 M diammonium phosphate, vapor diffusion, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.93	α = 90
b = 57.234	β = 101.07
c = 78.407	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	IMAGE PLATE	RIGAKU RAXIS		2013-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.28	38.47	99.9	0.127	13.3	7.3		18808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.36	100		0.011	2.1	7.1	1848

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	direct placement	THROUGHOUT	related to pdb entry 4O61	2.28	30	18790	934	99.76	0.2405	0.2382	0.24	0.2841	0.29	THIN SHELLS (SFTOOLS)	45.2232

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]
-2.05		0.85	1.87		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.915
r_dihedral_angle_4_deg	18.784
r_dihedral_angle_3_deg	14.775
r_dihedral_angle_1_deg	6.479
r_mcangle_it	1.559
r_angle_refined_deg	1.401
r_mcbond_it	0.935
r_mcbond_other	0.935
r_angle_other_deg	0.878
r_chiral_restr	0.077
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3248
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	45

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction