X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 24% PEG 4000, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.15 α = 90
b = 64.15 β = 90
c = 113.15 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Toroidal mirror 2006-11-12
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
2.2 35.4 91.6 0.094 0.094 -- 10.2 12643 11503 0.0 0.0 32.18
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)
2.2 2.32 87.1 0.235 0.235 2.9 10.6 1549

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 2.2 35.4 -- 0.0 11502 11502 561 90.98 0.198 0.198 0.196 0.232 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 2.2 2.257 787 46 741 0.18 0.215 -- 86.39
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 29.102
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.428
r_dihedral_angle_4_deg 18.897
r_xyhbond_nbd_refined 0.132
r_nbd_refined 0.194
r_dihedral_angle_2_deg 32.635
r_bond_refined_d 0.009
r_scangle_it 2.152
r_nbtor_refined 0.299
r_chiral_restr 0.081
r_scbond_it 1.392
r_angle_refined_deg 1.199
r_dihedral_angle_1_deg 4.444
r_mcangle_it 0.916
r_gen_planes_refined 0.004
r_mcbond_it 0.535
r_symmetry_hbond_refined 0.037
r_symmetry_vdw_refined 0.205
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1751
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 74

Software

Software
Software Name Purpose
SCALA data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
DNA data collection
MOSFLM data reduction
MOLREP phasing