2Z9A

Crystal Structure of Human Saposin C Dimer in Open Conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GTGpdb entry 2gtg

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429120 mM NaAcetate, 240 mM magnesium sulfate, 41% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.99α = 90
b = 48.99β = 90
c = 155.57γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4toroidal mirrors2004-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
12.52599.50.09418.83708847.985
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)
12.52.61000.5676.310030

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 DIFFRACTIONTHROUGHOUTpdb entry 2gtg2.52510030708733599.680.240.2390.271RANDOM46.373
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]
2.562.56-5.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.389
r_dihedral_angle_3_deg20.155
r_dihedral_angle_1_deg4.784
r_scangle_it2.773
r_scbond_it1.682
r_angle_refined_deg1.332
r_mcangle_it1.154
r_mcbond_it0.636
r_nbtor_refined0.301
r_symmetry_vdw_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.389
r_dihedral_angle_3_deg20.155
r_dihedral_angle_1_deg4.784
r_scangle_it2.773
r_scbond_it1.682
r_angle_refined_deg1.332
r_mcangle_it1.154
r_mcbond_it0.636
r_nbtor_refined0.301
r_symmetry_vdw_refined0.222
r_nbd_refined0.211
r_symmetry_hbond_refined0.202
r_xyhbond_nbd_refined0.153
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1212
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
MOLREPphasing