5KR7 | pdb_00005kr7

KDM4C bound to pyrazolo-pyrimidine scaffold

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	10-15% PEG 3350 0.2 magnesium chloride 0.1 HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.817	α = 90
b = 89.876	β = 90
c = 100.011	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	CCD	MARMOSAIC 225 mm CCD		2009-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	1.9	66.82	99.2	0.105	13.7	4		64012

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	3dxu	1.9	66.82	60706	3241	99.09	0.1945	0.1924	0.1924	0.2339	0.2341	RANDOM	26.056

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]
-0.01			0.58		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.782
r_dihedral_angle_3_deg	17.712
r_dihedral_angle_4_deg	16.036
r_dihedral_angle_1_deg	7.576
r_scbond_it	4.138
r_mcangle_it	3.555
r_mcbond_it	2.403
r_angle_refined_deg	1.467
r_chiral_restr	0.125
r_gen_planes_refined	0.018
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5565
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing