2GG3 | pdb_00002gg3

Novel bacterial methionine aminopeptidase inhibitors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GG2	PDB ENTRY 2GG2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, batch, pH 7.0, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.045	α = 90
b = 62.744	β = 108.85
c = 52.667	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	CCD	ADSC QUANTUM 4		2002-01-01	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	24.92	96.4	0.031	18.7	2.5	40960	40960

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.45	1.55	85.3		0.235	4.23	1.2	6408

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 2GG2	1.45	24.92	40960	40960	2076	96.38	0.126	0.124	0.124	0.13	0.161	0.16	RANDOM	15.946

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]
-0.41		0.45	0.42		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.106
r_dihedral_angle_4_deg	19.284
r_sphericity_free	12.261
r_dihedral_angle_3_deg	12.055
r_scangle_it	6.24
r_dihedral_angle_1_deg	6.08
r_sphericity_bonded	5.828
r_scbond_it	4.414
r_mcangle_it	2.967
r_rigid_bond_restr	2.098
r_mcbond_it	2.084
r_angle_refined_deg	1.719
r_mcbond_other	1.168
r_angle_other_deg	0.744
r_symmetry_vdw_other	0.383
r_symmetry_vdw_refined	0.253
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.217
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.178
r_chiral_restr	0.091
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.069
r_metal_ion_refined	0.044
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2105
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SCALEPACK	data scaling
AMoRE	phasing