X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 4.5
Temperature 293.0
Details 20.0% PEG-400, 0.2M Ca(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.08 α = 90
b = 109.22 β = 119.23
c = 112.6 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 flat mirror 2004-05-24
Diffraction Radiation
Monochromator Protocol
single crystal Si(311) bent monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- SSRL BL11-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.27 29.03 47.8 -- 0.086 -- 3.6 -- 61963 -- -- 46.59
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.27 2.39 38.4 -- 0.507 2.0 2.5 7228

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.27 29.03 -- -- -- 58811 3151 95.49 -- 0.17334 0.17127 0.21256 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.27 2.329 -- 185 3220 0.261 0.32 -- 71.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.509
Anisotropic B[1][1] 1.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.6
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.64
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.596
r_xyhbond_nbd_refined 0.175
r_scbond_it 3.936
r_scangle_it 5.093
r_gen_planes_other 0.003
r_bond_refined_d 0.014
r_mcbond_other 0.526
r_dihedral_angle_4_deg 17.957
r_symmetry_vdw_refined 0.196
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.804
r_dihedral_angle_3_deg 14.438
r_chiral_restr 0.089
r_nbd_other 0.177
r_nbtor_other 0.086
r_nbtor_refined 0.176
r_angle_other_deg 0.919
r_mcbond_it 1.237
r_mcangle_it 1.742
r_symmetry_hbond_refined 0.187
r_bond_other_d 0.003
r_nbd_refined 0.196
r_dihedral_angle_2_deg 35.816
r_symmetry_vdw_other 0.205
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6730
Nucleic Acid Atoms 0
Heterogen Atoms 275
Solvent Atoms 529

Software

Software
Software Name Purpose
XDS data scaling
XSCALE data scaling
SCALA data scaling version: 4.2)
MOLREP phasing
REFMAC refinement version: 5.2.0005
XDS data reduction
CCP4 data scaling version: (SCALA)