X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.3 α = 90
b = 88.52 β = 90
c = 118.88 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 mirrors --
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
1.58 50 98.9 -- 0.095 -- 6.8 70618 69842 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)
1.58 1.64 93.5 -- 0.493 -- 3.0 6484

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
MOLREP 1.58 50.0 -- -- 70614 66026 3501 98.46 -- 0.16763 0.16622 0.19434 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 1.58 1.621 4698 253 4445 0.232 0.271 -- 91.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.551
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.818
r_dihedral_angle_4_deg 19.777
r_scbond_it 4.334
r_chiral_restr 0.111
r_gen_planes_refined 0.009
r_dihedral_angle_3_deg 14.126
r_bond_refined_d 0.011
r_angle_refined_deg 1.481
r_mcbond_it 1.789
r_dihedral_angle_2_deg 26.255
r_mcangle_it 2.787
r_scangle_it 6.452
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4086
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 431

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling