2GG7 | pdb_00002gg7

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	batch	7	298	10 mg/ml protein, 25% PEG 8000, 100 mM TRIS-HCl, 1-5 mM inhibitor, pH 7.0, batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.123	α = 90
b = 62.945	β = 109.01
c = 52.743	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

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	1.12	23.98	93.2	0.021	28.1	2.6	91914	91914

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)
	1.12	1.25	73.2		0.082	11.2	1.5	25659

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	1.12	23.98	91867	91867	4597	99.14	0.133	0.132	0.132	0.14	0.155	0.16	RANDOM	11.436

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]
-0.22		0.24	0.38		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.559
r_dihedral_angle_4_deg	18.141
r_dihedral_angle_3_deg	11.581
r_sphericity_free	9.599
r_dihedral_angle_1_deg	6.013
r_sphericity_bonded	5.375
r_scangle_it	4.354
r_scbond_it	3.001
r_mcangle_it	2.27
r_angle_refined_deg	1.64
r_mcbond_it	1.585
r_rigid_bond_restr	1.483
r_mcbond_other	1.053
r_angle_other_deg	0.727
r_symmetry_vdw_other	0.372
r_nbd_refined	0.229
r_nbd_other	0.193
r_symmetry_hbond_refined	0.186
r_nbtor_refined	0.176
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.164
r_metal_ion_refined	0.164
r_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2224
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	21

Software

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