2CHD

Crystal structure of the C2A domain of Rabphilin-3A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125% PEG4000, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH=4.6
Crystal Properties
Matthews coefficientSolvent content
2.139.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.87α = 90
b = 39.16β = 90
c = 88.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKER SMART 6000OSMIC FOCUSING MIRRORS2005-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER ROTATING ANODE

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
11.9244.4197.80.05196.13104352
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)
11.921.9592.60.2832.74

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 1RSY1.9244.41990948897.80.2010.1980.269RANDOM22.01
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]
1.830.42-2.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.67
r_dihedral_angle_3_deg16.521
r_dihedral_angle_4_deg14.998
r_dihedral_angle_1_deg7.436
r_scangle_it4.292
r_scbond_it2.822
r_angle_refined_deg1.752
r_mcangle_it1.746
r_mcbond_it1.104
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.67
r_dihedral_angle_3_deg16.521
r_dihedral_angle_4_deg14.998
r_dihedral_angle_1_deg7.436
r_scangle_it4.292
r_scbond_it2.822
r_angle_refined_deg1.752
r_mcangle_it1.746
r_mcbond_it1.104
r_nbtor_refined0.323
r_nbd_refined0.257
r_symmetry_hbond_refined0.252
r_xyhbond_nbd_refined0.201
r_symmetry_vdw_refined0.191
r_chiral_restr0.139
r_bond_refined_d0.018
r_gen_planes_refined0.008
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1020
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing