6CG1 | pdb_00006cg1

Crystal Structure of KDM4A with Compound 14

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VGI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.582	α = 90
b = 101.651	β = 99.73
c = 142.43	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	77	CCD	ADSC QUANTUM 315		2012-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	1.0	APS	14-BM-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.16	140.38	98.6	0.095	11.52	3.6		86464

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.29	93.3		0.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	5VGI	2.16	140.38	86464	4327	99.2	0.1782	0.1749	0.1829	0.2403	0.2444	RANDOM	40.985

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]
-1.21		-1.13	-0.23		1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.109
r_dihedral_angle_4_deg	19.45
r_dihedral_angle_3_deg	17.153
r_dihedral_angle_1_deg	6.744
r_angle_refined_deg	1.781
r_angle_other_deg	1.117
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11267
Nucleic Acid Atoms
Solvent Atoms	821
Heterogen Atoms	80

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing