3EJV

Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52772.0000M (NH4)2SO4, 2.0000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.54α = 90
b = 79.54β = 90
c = 79.54γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-08-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91162,0.97929SSRLBL9-2

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
11.428.12799.30.04813.9933205-313.35
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)
1.41.45970.552

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.428.12733165167299.870.1430.1420.161RANDOM16.11
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_dihedral_angle_2_deg33.973
r_dihedral_angle_4_deg17.2
r_dihedral_angle_3_deg11.86
r_dihedral_angle_1_deg6.624
r_sphericity_free6.287
r_sphericity_bonded3.057
r_scangle_it2.888
r_mcangle_it2.606
r_scbond_it2.131
r_mcbond_it1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.973
r_dihedral_angle_4_deg17.2
r_dihedral_angle_3_deg11.86
r_dihedral_angle_1_deg6.624
r_sphericity_free6.287
r_sphericity_bonded3.057
r_scangle_it2.888
r_mcangle_it2.606
r_scbond_it2.131
r_mcbond_it1.99
r_angle_refined_deg1.545
r_rigid_bond_restr1.363
r_angle_other_deg0.971
r_mcbond_other0.859
r_symmetry_vdw_other0.295
r_nbd_refined0.223
r_nbd_other0.214
r_symmetry_vdw_refined0.186
r_nbtor_refined0.172
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.136
r_chiral_restr0.112
r_nbtor_other0.086
r_bond_refined_d0.015
r_bond_other_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1203
Nucleic Acid Atoms
Solvent Atoms174
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHARPphasing