3ERB

The Crystal Structure of C2b, a Fragment of Complement Component C2 produced during C3-convertase Formation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OK5PDB ENTRY 2OK5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27718% PEG 3350, 0.22M Sodium Chloride, 0.02M Betaine Hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7154.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.06α = 90
b = 60.06β = 90
c = 61.687γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.8401000.033214.3623095
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)
1.81.861000.2375.14.15

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2OK51.821.5221882118299.90.215520.21420.23963RANDOM23.257
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]
0.220.110.22-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.163
r_dihedral_angle_4_deg16.708
r_dihedral_angle_3_deg12.198
r_dihedral_angle_1_deg6.3
r_scangle_it3.341
r_scbond_it2.07
r_angle_refined_deg1.243
r_mcangle_it1.157
r_mcbond_it0.813
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.163
r_dihedral_angle_4_deg16.708
r_dihedral_angle_3_deg12.198
r_dihedral_angle_1_deg6.3
r_scangle_it3.341
r_scbond_it2.07
r_angle_refined_deg1.243
r_mcangle_it1.157
r_mcbond_it0.813
r_nbtor_refined0.301
r_nbd_refined0.203
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.128
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1415
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing