3MX6 | pdb_00003mx6

Crystal structure of methionine aminopeptidase from Rickettsia prowazekii bound to methionine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MR1	PDB ENTRY 3MR1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 M sodium sulfate, 0.1 M BisTris propane, 20% PEG 3350, 20% ethylene glycol as cryo-protectant, 25.2 mg/mL protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.37	α = 90
b = 67.55	β = 97.429
c = 80.89	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 315		2010-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97946	ALS	5.0.1

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	1.7	20	97.9	0.049	21.52	4.8		58037		-3	19.463

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	1.7	1.74	82.3		0.185	5.9	3.9

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 (All)	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 3MR1	1.7	19.983	57977	2932	97.794	0.162	0.1597	0.1724	0.1985	0.2096	RANDOM	14.205

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]
0.002		-0.002	0.001		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.829
r_dihedral_angle_3_deg	11.537
r_dihedral_angle_1_deg	6.408
r_lrange_it	5.233
r_lrange_other	5.061
r_scangle_it	3.583
r_scangle_other	3.582
r_scbond_it	2.324
r_scbond_other	2.323
r_mcangle_other	1.788
r_mcangle_it	1.78
r_mcbond_it	1.169
r_mcbond_other	1.164
r_angle_refined_deg	1.141
r_angle_other_deg	0.443
r_nbd_refined	0.205
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.132
r_nbd_other	0.129
r_symmetry_nbd_refined	0.106
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.061
r_symmetry_xyhbond_nbd_other	0.059
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4086
Nucleic Acid Atoms
Solvent Atoms	726
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction