9FIM | pdb_00009fim

compound 1 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	1.1 M Na3Citrate, 0.1M Tris 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.027	α = 90
b = 110.027	β = 90
c = 129.737	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		2018-10-12	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	1.6	47.64	100	0.076	1	29.8	39		61536

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	1.6	1.63	100		0.765

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	1.6	47.64	61468	3057	99.99	0.16	0.159	0.1641	0.1866	0.1657	29.863

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]
-0.225	-0.113		-0.225		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.775
r_lrange_it	14.345
r_lrange_other	14.301
r_dihedral_angle_3_deg	12.352
r_scangle_it	10.733
r_scangle_other	10.731
r_mcangle_other	7.959
r_mcangle_it	7.947
r_scbond_it	7.358
r_scbond_other	7.356
r_dihedral_angle_2_deg	7.065
r_dihedral_angle_1_deg	6.467
r_mcbond_it	5.303
r_mcbond_other	5.272
r_rigid_bond_restr	3.835
r_angle_refined_deg	1.856
r_angle_other_deg	0.612
r_nbd_refined	0.231
r_nbd_other	0.209
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.141
r_dihedral_angle_other_2_deg	0.128
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.085
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	2435
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	33

Software

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