5YPD | pdb_00005ypd

Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N 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% Peg 3350, 3% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.226	α = 90
b = 44.909	β = 94.17
c = 57.295	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++		2015-09-01	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	1.62	28.57	90.7	0.044	0.062	0.044	0.996	34	1.9		29506

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	1.62	1.68	83.2		0.2	0.283	0.2	0.896		1.9

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	1.62	28.57	28109	1396	92.45	0.1461	0.1444	0.1444	0.1818	0.1821	RANDOM	26.91

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	39.158
r_dihedral_angle_4_deg	21.386
r_dihedral_angle_3_deg	12.058
r_dihedral_angle_1_deg	6.297
r_angle_refined_deg	2.106
r_angle_other_deg	1.082
r_chiral_restr	0.136
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2154
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	25

Software

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