1GNY | pdb_00001gny

xylan-binding module CBM15


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherPARTIAL MODEL (UNPUBLISHED)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.2M NH4OAC,0.1M NA CITRATE PH 5.6, 30% POLYETHYLENE GLYCOL 4000
Crystal Properties
Matthews coefficientSolvent content
2.856.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.15α = 90
b = 60.122β = 102.78
c = 33.107γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2001-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
11.6350980.043293.621535-3
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)
11.631.69800.3332.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPARTIAL MODEL (UNPUBLISHED)1.635020424110997.60.1520.150.160.177RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.243
r_scbond_it2.512
r_angle_other_deg1.726
r_mcangle_it1.587
r_dihedral_angle_3_deg1.182
r_mcbond_it0.871
r_metal_ion_refined0.447
r_nbd_refined0.186
r_nbd_other0.163
r_symmetry_vdw_other0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.243
r_scbond_it2.512
r_angle_other_deg1.726
r_mcangle_it1.587
r_dihedral_angle_3_deg1.182
r_mcbond_it0.871
r_metal_ion_refined0.447
r_nbd_refined0.186
r_nbd_other0.163
r_symmetry_vdw_other0.15
r_symmetry_hbond_refined0.116
r_chiral_restr0.106
r_xyhbond_nbd_refined0.087
r_nbtor_other0.085
r_symmetry_vdw_refined0.037
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1121
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing