X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 8% PEG6000, 5% MPD, 0.1M Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.99 α = 90
b = 88.19 β = 90
c = 121.23 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE mirros 2010-05-23
Diffraction Radiation
Monochromator Protocol
Rotated-inclined double-crystal monochromator , Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00 SPRING-8 BL41XU

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
1.45 50 100.0 -- 0.053 -- 5.3 91864 91864 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)
1.45 1.5 100.0 -- 0.617 3.3 6.4 9084

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 1.45 25.62 -- -- -- 86870 4583 99.7 -- 0.16209 0.16041 0.19378 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 1.45 1.489 -- 321 6305 0.231 0.256 -- 99.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.313
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.264
r_scbond_it 3.522
r_mcangle_it 2.455
r_mcbond_it 1.466
r_gen_planes_refined 0.015
r_chiral_restr 0.176
r_dihedral_angle_4_deg 18.593
r_dihedral_angle_3_deg 13.23
r_dihedral_angle_2_deg 28.186
r_dihedral_angle_1_deg 5.806
r_angle_refined_deg 2.54
r_bond_refined_d 0.029
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4073
Nucleic Acid Atoms 0
Heterogen Atoms 59
Solvent Atoms 452

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
MOLREP model building
HKL-2000 data collection