8OXG | pdb_00008oxg

Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D6F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.05	α = 90
b = 101.127	β = 98.755
c = 83.737	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2022-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.73	44.84	99.6	0.089	0.105	0.055	0.998	12.5	6.9		101909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.76	92.3		1.288	0.866	0.649		5.7

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	1.731	44.84	101840	5131	99.836	0.183	0.1811	0.19	0.215	0.23	28.255

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]
2.949		0.841	-1.827		-1.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.512
r_dihedral_angle_6_deg	17.142
r_dihedral_angle_3_deg	14.94
r_lrange_it	7.442
r_lrange_other	7.373
r_dihedral_angle_1_deg	7.169
r_dihedral_angle_other_2_deg	6.07
r_scangle_it	6.048
r_scangle_other	6.048
r_mcangle_it	4.488
r_mcangle_other	4.488
r_scbond_it	4.459
r_scbond_other	4.458
r_mcbond_it	3.558
r_mcbond_other	3.558
r_angle_refined_deg	2.13
r_angle_other_deg	0.739
r_nbd_other	0.238
r_nbd_refined	0.222
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.182
r_symmetry_nbd_refined	0.174
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.147
r_chiral_restr	0.132
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.034
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5779
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms	64

Software

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