2PVZ

Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	300-350 mM NaCl, 21-24% methyl ether poly(ethylene glycol) 5000, buffered with 100 mM triethanolamine (pH 8.0 at 25 C). , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.868	α = 90
b = 104.058	β = 104.37
c = 78.254	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			2005-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.964108	APS	19-BM

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	1.97	75.81	98.2	0.029	21.1	1.9		204015

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	1.97	2.02	95.5		0.074	9.1	1.7	3643

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	75.81	53215	2850	98.65	0.15937	0.15788	0.18769	RANDOM	14.034

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]
-0.2		-0.28	0.3		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.272
r_dihedral_angle_4_deg	14.276
r_dihedral_angle_3_deg	11.853
r_dihedral_angle_1_deg	5.361
r_scangle_it	1.775
r_scbond_it	1.109
r_angle_refined_deg	1.073
r_mcangle_it	0.717
r_mcbond_it	0.433
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.272
r_dihedral_angle_4_deg	14.276
r_dihedral_angle_3_deg	11.853
r_dihedral_angle_1_deg	5.361
r_scangle_it	1.775
r_scbond_it	1.109
r_angle_refined_deg	1.073
r_mcangle_it	0.717
r_mcbond_it	0.433
r_nbtor_refined	0.301
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5649
Nucleic Acid Atoms
Solvent Atoms	849
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.