4XDP | pdb_00004xdp

Crystal structure of human KDM4C catalytic domain bound to tris

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291.15	0.8 M Lithium chloride, 0.1 M TRIS pH 8.5, 28 % w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.87	α = 90
b = 89.75	β = 96.31
c = 98.28	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARMOSAIC 300 mm CCD		2013-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.07	31.42	98.6	0.124	0.068	0.995	11	4.3		48744

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.12	97.8		0.669	0.366	0.733	2.3	4.3	3558

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.07	31.42	48738	2463	98.55	0.2084	0.2066	0.21	0.242	0.25	RANDOM	27.402

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]
0.86		0.3	-0.36		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.83
r_dihedral_angle_3_deg	14.93
r_dihedral_angle_4_deg	14.778
r_dihedral_angle_1_deg	6.212
r_angle_refined_deg	1.367
r_mcangle_it	0.936
r_angle_other_deg	0.767
r_mcbond_it	0.523
r_mcbond_other	0.522
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5548
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	73

Software

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