7VJV | pdb_00007vjv

Human AlkB homolog ALKBH6 in complex with alpha-katoglutarate and Mn

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3THP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG 8000, Tris

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.118	α = 90
b = 64.407	β = 90
c = 88.416	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2019-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	50	98.67	0.977	15	4.5		27487

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	1.75	1.78			0.827

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3THP	1.75	26.417	26981	1372	98.929	0.191	0.1901	0.2	0.2068	0.21	20.296

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]
-0.003			0.01		-0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.252
r_dihedral_angle_4_deg	12.99
r_dihedral_angle_3_deg	12.27
r_dihedral_angle_1_deg	7.304
r_lrange_it	4.738
r_lrange_other	4.716
r_scangle_it	3.957
r_scangle_other	3.956
r_mcangle_other	2.6
r_mcangle_it	2.589
r_scbond_it	2.552
r_scbond_other	2.552
r_mcbond_it	1.731
r_mcbond_other	1.7
r_angle_refined_deg	1.495
r_angle_other_deg	1.329
r_nbd_refined	0.209
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.163
r_symmetry_nbd_refined	0.162
r_nbd_other	0.129
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_refined	0.055
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1707
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing