X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.6
Temperature 293.0
Details 1.3 M sodium citrate, 0.1M hepes, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.44 α = 90
b = 36.44 β = 90
c = 78.78 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-09-19
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B -- NSLS X12B

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
1.27 50 97.6 0.044 0.036 -- 7.5 14732 14379 2.0 2.0 --
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)
1.27 1.32 93.5 0.386 -- -- 5.4 --

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 1.35 25.77 -- -- -- 11423 586 97.65 -- 0.1938 0.19226 0.2238 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 1.35 1.385 -- 57 814 0.252 0.292 -- 99.54
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.119
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 1.073
r_gen_planes_other 0.001
r_nbd_refined 0.217
r_chiral_restr 0.096
r_dihedral_angle_2_deg 37.147
r_dihedral_angle_4_deg 7.731
r_bond_other_d 0.002
r_mcbond_it 2.349
r_scbond_it 4.083
r_sphericity_bonded 4.441
r_mcbond_other 0.917
r_dihedral_angle_1_deg 6.595
r_dihedral_angle_3_deg 14.316
r_nbtor_refined 0.192
r_symmetry_hbond_refined 0.079
r_angle_refined_deg 1.711
r_xyhbond_nbd_refined 0.144
r_bond_refined_d 0.019
r_symmetry_vdw_refined 0.066
r_rigid_bond_restr 3.18
r_scangle_it 4.502
r_sphericity_free 9.964
r_gen_planes_refined 0.01
r_symmetry_vdw_other 0.225
r_mcangle_it 2.954
r_nbtor_other 0.09
r_nbd_other 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 365
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 36

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
HKL-2000 data reduction
MOLREP phasing