2GLK | pdb_00002glk

High-resolution study of D-Xylose isomerase, 0.94A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	50mM tris-HCl,25%AMSO4,2mM Mn2+ and 2mM Co2+ , XI @ 25mg/ml., pH 8, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.712	α = 90
b = 97.935	β = 90
c = 101.867	γ = 90

Symmetry
Space Group	I 2 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	MAR CCD 165 mm		2001-09-08	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)	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	0.94	35.36	85.6			252079	252079

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.944	0.965	12

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	1XIB	0.94	35.36	252079	231037	21042	85.59	0.1157	0.1157	0.11458	0.11	0.12792	0.13	RANDOM	11.123

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]
0.21			-0.11		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.824
r_dihedral_angle_4_deg	13.787
r_dihedral_angle_3_deg	12.414
r_sphericity_free	11.867
r_sphericity_bonded	5.914
r_dihedral_angle_1_deg	5.472
r_scangle_it	4.695
r_scbond_it	3.436
r_mcangle_it	2.56
r_mcbond_it	2.118
r_angle_refined_deg	1.917
r_angle_other_deg	1.869
r_rigid_bond_restr	1.842
r_mcbond_other	1.316
r_symmetry_vdw_other	0.34
r_symmetry_vdw_refined	0.3
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.207
r_nbd_other	0.205
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.112
r_nbtor_other	0.095
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3054
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
X-GEN	data reduction
HKL-2000	data scaling
AMoRE	phasing