X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 12% PEG 8000, 400 mM Ammonium sulfate, 100 mM MES/Malic Acid/ Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.5 α = 90
b = 100.5 β = 90
c = 161.3 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 315r -- 2009-01-15
Diffraction Radiation
Monochromator Protocol
single crystal Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.979 SSRL BL7-1

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
3.5 30 98.4 0.119 -- -- 3.8 10843 10670 0.0 0.0 --
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)
3.5 3.69 99.7 0.26 -- 2.8 3.8 --

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 3.5 29.57 -- 0.0 10843 10158 511 -- -- 0.21519 0.2124 0.26997 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 3.5 3.59 -- 28 774 0.244 0.24 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.266
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.741
r_scbond_it 0.988
r_mcangle_it 1.146
r_mcbond_it 0.638
r_symmetry_hbond_refined 0.132
r_bond_refined_d 0.012
r_angle_refined_deg 1.531
r_dihedral_angle_1_deg 7.431
r_dihedral_angle_2_deg 40.734
r_dihedral_angle_3_deg 21.601
r_dihedral_angle_4_deg 19.257
r_chiral_restr 0.104
r_gen_planes_refined 0.004
r_nbd_refined 0.248
r_nbtor_refined 0.322
r_xyhbond_nbd_refined 0.185
r_symmetry_vdw_refined 0.215
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4175
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 0

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Refmac Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
Refmac model building
Blu-Ice data collection