2BB7 | pdb_00002bb7

Mn Form Of E. coli Methionine Aminopeptidase In Complex With a quinolinyl sulfonamide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XNZ	pdb entry 1XNZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.039	α = 90
b = 60.416	β = 104.4
c = 50.521	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		2005-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.7	18.86	98.8	0.037	0.037	11.5	3.6		24139

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.79	97.2	97.2	0.158	0.158	4.6	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	pdb entry 1XNZ	1.7	17.62	22887	24120	1233	98.63	0.19	0.19	0.187	0.19	0.233	0.23	RANDOM	24.426

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]
		0.01	0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.253
r_dihedral_angle_4_deg	15.655
r_dihedral_angle_3_deg	11.741
r_dihedral_angle_1_deg	6.375
r_scangle_it	3.748
r_scbond_it	2.333
r_angle_refined_deg	1.415
r_mcangle_it	1.413
r_mcbond_it	0.832
r_symmetry_hbond_refined	0.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.253
r_dihedral_angle_4_deg	15.655
r_dihedral_angle_3_deg	11.741
r_dihedral_angle_1_deg	6.375
r_scangle_it	3.748
r_scbond_it	2.333
r_angle_refined_deg	1.415
r_mcangle_it	1.413
r_mcbond_it	0.832
r_symmetry_hbond_refined	0.373
r_nbtor_refined	0.302
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.191
r_metal_ion_refined	0.153
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2007
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	19

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.