9FJT | pdb_00009fjt

Human Monoamine Oxidase B in complex with MC4762 inhibitor (9a) at 1.4 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277.15	12 % (w/v) PEG 4000, 100 mM ADA buffer pH 6.5, 70 mM Lithium Sulfate, 4.5 mM Zwittergent 3-12

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.92	α = 90
b = 222.033	β = 90
c = 85.879	γ = 90

Symmetry
Space Group	C 2 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 PILATUS3 2M		2022-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

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	1.4	47.18	99.8	0.087	0.998	12.9	6.4		243584

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42	100		1.081	0.627	1.7	6.8

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	1.4	47.18	243471	6176	99.706	0.167	0.1667	0.1762	0.1899	0.1977	15.064

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]
0.585			-0.428		-0.157

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.336
r_dihedral_angle_other_3_deg	19.871
r_dihedral_angle_4_deg	14.488
r_dihedral_angle_3_deg	12.679
r_dihedral_angle_1_deg	6.497
r_lrange_it	5.387
r_lrange_other	5.225
r_scangle_it	4.208
r_scangle_other	4.208
r_scbond_it	2.797
r_scbond_other	2.797
r_mcangle_it	1.942
r_mcangle_other	1.942
r_angle_other_deg	1.933
r_angle_refined_deg	1.93
r_mcbond_it	1.358
r_mcbond_other	1.356
r_nbd_other	0.338
r_nbd_refined	0.231
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.106
r_symmetry_nbd_refined	0.096
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr_other	0.068
r_xyhbond_nbd_other	0.036
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7911
Nucleic Acid Atoms
Solvent Atoms	973
Heterogen Atoms	187

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing