2RKQ

Crystal structure of drosophila peptidoglycan recognition protein SD (PGRP-SD)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629325% PEG-mme 2000, 0.1M MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.559α = 90
b = 57.438β = 90
c = 71.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.52099.60.073103.8254902538018.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.5598.70.3263.83.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S2J1.5202549024154127399.750.155670.154710.17328RANDOM17.816
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]
-0.54-0.370.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.02
r_dihedral_angle_4_deg20.01
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg5.692
r_scangle_it3.548
r_scbond_it2.281
r_angle_refined_deg1.363
r_mcangle_it1.248
r_mcbond_it0.748
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.02
r_dihedral_angle_4_deg20.01
r_dihedral_angle_3_deg11.301
r_dihedral_angle_1_deg5.692
r_scangle_it3.548
r_scbond_it2.281
r_angle_refined_deg1.363
r_mcangle_it1.248
r_mcbond_it0.748
r_nbtor_refined0.311
r_symmetry_vdw_refined0.255
r_nbd_refined0.207
r_xyhbond_nbd_refined0.189
r_symmetry_hbond_refined0.145
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1304
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing