9FKM | pdb_00009fkm

compound 2b bound KMT9 crystal structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6H1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.8 M (NH4)2SO4, 0.1M Bis-Tris 6.75

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.444	α = 90
b = 110.444	β = 90
c = 130.507	γ = 120

Symmetry
Space Group	P 61 2 2

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-F		2019-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	47.82	100	0.229	0.999	15.9	39.2		75058

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	1.5	1.53			0.455

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.502	47.82	74984	3699	99.925	0.183	0.1818	0.1964	0.2014	0.214	20.371

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]
0.076	0.038		0.076		-0.246

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.189
r_dihedral_angle_3_deg	12.654
r_dihedral_angle_2_deg	10.604
r_dihedral_angle_1_deg	6.303
r_lrange_it	5.313
r_lrange_other	5.264
r_scangle_it	4.329
r_scangle_other	4.328
r_scbond_it	2.829
r_scbond_other	2.828
r_angle_refined_deg	2.072
r_mcangle_other	1.952
r_mcangle_it	1.95
r_mcbond_it	1.321
r_mcbond_other	1.289
r_angle_other_deg	0.729
r_nbd_refined	0.227
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.179
r_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.17
r_chiral_restr	0.126
r_symmetry_nbd_refined	0.118
r_xyhbond_nbd_refined	0.115
r_dihedral_angle_other_2_deg	0.096
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2418
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing