X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 293.0
Details 2.5-2.7M ammonium sulfate, 0.1M sodium citrate (pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.78 α = 90
b = 73.46 β = 120.05
c = 81.25 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPRING-8 BL44XU

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
1.76 50 99.7 0.048 -- -- 3.8 -- 65324 -- -- --
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)
1.76 1.82 100.0 0.23 -- -- 3.8 6506

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 1.76 34.91 -- -- -- 62003 3308 99.5 -- 0.18652 0.18444 0.22612 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 1.764 1.809 -- 228 4458 0.248 0.289 -- 97.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.808
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] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 6.326
r_scbond_it 4.21
r_mcangle_it 2.989
r_mcbond_it 1.824
r_gen_planes_refined 0.015
r_chiral_restr 0.225
r_dihedral_angle_4_deg 22.382
r_dihedral_angle_3_deg 15.418
r_dihedral_angle_2_deg 29.486
r_dihedral_angle_1_deg 7.293
r_angle_refined_deg 2.753
r_bond_refined_d 0.034
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3811
Nucleic Acid Atoms 0
Heterogen Atoms 190
Solvent Atoms 177

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
HKL data reduction