9Z4X | pdb_00009z4x

MENIN IN COMPLEX WITH JNJ-75276617 (Bleximenib)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	100 mM Tris pH 6.75 , 5 M NaCl , 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.372	α = 90
b = 70.486	β = 91.68
c = 145.561	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	100	PIXEL	DECTRIS PILATUS 6M		2020-01-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9796	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.95	145.5	89.9	0.16	0.185	6.9	3.8		40857

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.96	3.2	51.2		0.849	0.998	1.4	3.5

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	2.95	145.5	38841	2014	89.9	0.23659	0.23333	0.2342	0.29695	0.2942	RANDOM

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]
-1.77		-0.95	2.45		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.126
r_dihedral_angle_3_deg	12.882
r_dihedral_angle_4_deg	12.171
r_long_range_B_refined	7.999
r_long_range_B_other	7.998
r_mcangle_it	5.799
r_mcangle_other	5.798
r_dihedral_angle_1_deg	5.485
r_scangle_other	5.483
r_mcbond_it	3.543
r_mcbond_other	3.543
r_scbond_it	3.352
r_scbond_other	3.35
r_angle_refined_deg	1.097
r_angle_other_deg	0.889
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15264
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	199

Software

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