X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.1M Tris-HCl pH 8.5, 0.2M Ammonium phosphate monobasic, 50% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.21 α = 90
b = 114.83 β = 109.74
c = 102.22 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 mirrors 2010-04-08
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1

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
2.3 50 98.9 0.157 -- -- 3.7 -- 71172 -- -3.0 --
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)
2.3 2.38 98.3 0.392 -- 2.8 3.7 --

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 2.3 32.46 -- -- -- 67472 3588 96.66 -- 0.21155 0.20963 0.24871 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 2.3 2.359 -- 198 3500 0.303 0.333 -- 68.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.703
Anisotropic B[1][1] 0.98
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.68
Anisotropic B[2][2] -0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.09
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.701
r_dihedral_angle_3_deg 19.024
r_gen_planes_refined 0.017
r_mcangle_it 2.771
r_dihedral_angle_1_deg 8.37
r_angle_refined_deg 0.897
r_bond_refined_d 0.007
r_scangle_it 6.8
r_scbond_it 4.682
r_dihedral_angle_2_deg 35.182
r_chiral_restr 0.079
r_dihedral_angle_4_deg 19.167
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8940
Nucleic Acid Atoms 0
Heterogen Atoms 105
Solvent Atoms 158

Software

Software
Software Name Purpose
BL38B1 data collection version: BSS
MOLREP phasing
REFMAC refinement version: 5.5.0102
DENZO data reduction
SCALEPACK data scaling