5YOI | pdb_00005yoi

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105T mutant) in complex with Methionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1M Hepes, 27% Peg3350, 3% glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.236	α = 90
b = 48.653	β = 95.34
c = 56.052	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	IMAGE PLATE	RIGAKU RAXIS IV++		2016-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

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	1.63	28.54	97.8	0.034	0.046	0.031	0.998	26.5	1.9		33147			21.27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.69	94.3		0.232	0.308	0.2	0.92		1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1YJ3	1.63	28.54	33132	1558	99.85	0.16336	0.16112	0.18	0.21164	0.22	RANDOM	22.968

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.424
r_dihedral_angle_4_deg	16.786
r_dihedral_angle_3_deg	13.81
r_dihedral_angle_1_deg	6.026
r_long_range_B_refined	5.696
r_long_range_B_other	5.649
r_scangle_other	4.693
r_scbond_it	3.23
r_scbond_other	3.228
r_mcangle_it	2.843
r_mcangle_other	2.843
r_mcbond_it	2.121
r_mcbond_other	2.12
r_angle_refined_deg	2.103
r_angle_other_deg	1.107
r_chiral_restr	0.129
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2153
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	model building
PDB_EXTRACT	data extraction
DENZO	data reduction
DENZO	data processing
HKL-2000	phasing