9HTA | pdb_00009hta

Dispersin from Terribacillus saccharophilus Dispts2 in complex with NAG-thiazoline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8QB6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293MPD screen E7: 0.1 M Citric acid pH 4.0, 20% MPD
Crystal Properties
Matthews coefficientSolvent content
3.0259.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.06α = 90
b = 90.06β = 90
c = 98.12γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1740.9393.10.090.0990.040.99913.311.623157
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.172.2476.44.7355.212.1510.5320.511.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.1740.92623065108992.8950.2140.21210.21220.25280.252759.004
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]
0.5950.2980.595-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.536
r_dihedral_angle_3_deg13.6
r_lrange_it9.215
r_lrange_other9.215
r_dihedral_angle_2_deg7.533
r_dihedral_angle_1_deg6.994
r_scangle_it6.978
r_scangle_other6.976
r_mcangle_it6.432
r_mcangle_other6.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.536
r_dihedral_angle_3_deg13.6
r_lrange_it9.215
r_lrange_other9.215
r_dihedral_angle_2_deg7.533
r_dihedral_angle_1_deg6.994
r_scangle_it6.978
r_scangle_other6.976
r_mcangle_it6.432
r_mcangle_other6.43
r_mcbond_it4.642
r_mcbond_other4.641
r_scbond_it4.568
r_scbond_other4.564
r_angle_refined_deg1.482
r_angle_other_deg0.564
r_nbd_refined0.207
r_nbtor_refined0.182
r_symmetry_nbd_other0.176
r_nbd_other0.146
r_xyhbond_nbd_refined0.128
r_symmetry_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.074
r_chiral_restr0.069
r_symmetry_nbd_refined0.051
r_gen_planes_refined0.006
r_bond_refined_d0.005
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2631
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing