3KTC | pdb_00003ktc

Crystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.54 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2000M MgCl2, 10.0000% PEG-8000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.653	α = 90
b = 79.653	β = 90
c = 194.406	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97855,0.97799	SSRL	BL11-1

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	1.54	29.323	99.1	0.079	12.56			106036		-3	16.505

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	1.54	1.6	95		0.858	1.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.54	29.323	105995	5292	99.29	0.137	0.136	0.15	0.157	0.17	RANDOM	27.172

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]
0.12	0.06		0.12		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.633
r_dihedral_angle_4_deg	17.203
r_dihedral_angle_3_deg	11.935
r_dihedral_angle_1_deg	5.273
r_scangle_it	4.948
r_scbond_it	3.573
r_mcangle_it	2.069
r_mcbond_it	1.593
r_angle_refined_deg	1.517
r_angle_other_deg	1.06
r_mcbond_other	0.377
r_symmetry_vdw_other	0.261
r_nbd_refined	0.236
r_symmetry_vdw_refined	0.221
r_metal_ion_refined	0.22
r_nbd_other	0.189
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.174
r_symmetry_metal_ion_refined	0.146
r_chiral_restr	0.094
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5217
Nucleic Acid Atoms
Solvent Atoms	709
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing