3RMI | pdb_00003rmi

Crystal structure of Chorismate mutase from Bartonella henselae str. Houston-1 in complex with malate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D8E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	Internal tracking number 218208F3. INDEX screen condition F3: 5% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG-MME 5000. BaheA.00146.a.A1 PS00787 at 51.1 mg/ml., vapor diffusion, sitting drop, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.32	α = 90
b = 71.32	β = 90
c = 145.84	γ = 120

Symmetry
Space Group	P 62 2 2

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		2011-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.9765	ALS	5.0.3

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	2.4	19.8	98.9	0.047	27	7.8	9173	9071		-3	53.213

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)
	2.4	2.46	99.4		0.439	5.6	8.3	663

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 (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	2d8e	2.4	19.8	9173	9024	434	98.68	0.219	0.217	0.22	0.253	0.26	RANDOM	49.732

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]
3.23	1.62		3.23		-4.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.045
r_dihedral_angle_3_deg	16.736
r_dihedral_angle_4_deg	10.471
r_dihedral_angle_1_deg	4.911
r_scangle_it	3.508
r_scbond_it	2.104
r_angle_refined_deg	1.48
r_mcangle_it	1.259
r_angle_other_deg	0.902
r_mcbond_it	0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.045
r_dihedral_angle_3_deg	16.736
r_dihedral_angle_4_deg	10.471
r_dihedral_angle_1_deg	4.911
r_scangle_it	3.508
r_scbond_it	2.104
r_angle_refined_deg	1.48
r_mcangle_it	1.259
r_angle_other_deg	0.902
r_mcbond_it	0.61
r_mcbond_other	0.114
r_chiral_restr	0.075
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	838
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	19

Software

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

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.