1NQ6

Crystal Structure of the catalytic domain of xylanase A from Streptomyces halstedii JM8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E0WPDB ENTRY 1E0W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298PEG 4000, MAGNESIUM CHLORIDE, SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.6122.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.05α = 90
b = 79.6β = 90
c = 87.8γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCH1996-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.885EMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.78224.81897.10.04413.123589229059.453
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.8885.80.0848.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1E0W1.7824.822286521207165896.730.14840.147450.145150.17643RANDOM13.257
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]
0.33-0.80.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.029
r_scangle_it1.95
r_scbond_it1.245
r_angle_refined_deg1.09
r_mcangle_it0.717
r_mcbond_it0.387
r_nbd_refined0.191
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.029
r_scangle_it1.95
r_scbond_it1.245
r_angle_refined_deg1.09
r_mcangle_it0.717
r_mcbond_it0.387
r_nbd_refined0.191
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.111
r_xyhbond_nbd_refined0.1
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2297
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing