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 30% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.06 α = 86.41
b = 73.17 β = 87.62
c = 148.76 γ = 86.25
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2009-04-21
Diffraction Radiation
Monochromator Protocol
SI(111) DOUBLE MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.2000 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
3.2 50 97.8 -- 0.06 -- 4.3 27085 27085 -- 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)
3.2 3.31 94.0 -- 0.27 2.7 -- --

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 3.2 38.94 -- 0.0 25650 25650 1347 96.8 0.252 0.252 0.249 0.299 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 3.19 3.28 -- 98 1662 0.318 0.434 -- 85.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 127.92
Anisotropic B[1][1] -0.22
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.05
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] -0.13
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 0.865
r_dihedral_angle_1_deg 3.757
r_dihedral_angle_3_deg 15.175
r_bond_refined_d 0.008
r_dihedral_angle_4_deg 11.552
r_gen_planes_refined 0.004
r_chiral_restr 0.054
r_dihedral_angle_2_deg 31.551
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11320
Nucleic Acid Atoms 0
Heterogen Atoms 185
Solvent Atoms 0

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.6.0117
HKL-2000 data reduction
HKL-2000 data scaling