X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 289.15
Details 8% PEG 4000, 0.1M sodium acetate trihydrate (pH 4.6) , VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.78 α = 90
b = 88.76 β = 102.68
c = 86.49 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 MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U

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
2.5 50 98.5 0.075 0.075 -- 3.7 28894 28461 0.0 -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)
2.5 2.59 90.4 0.166 0.166 7.4 3.5 --

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 2.51 50.0 -- -- 27475 26989 1445 98.23 -- 0.23239 0.2301 0.27556 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 2.505 2.57 -- 110 1772 0.251 0.344 -- 87.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.854
Anisotropic B[1][1] -3.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.34
Anisotropic B[2][2] 5.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.51
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.422
r_scbond_it 0.24
r_mcangle_it 0.278
r_mcbond_it 0.151
r_gen_planes_refined 0.004
r_chiral_restr 0.054
r_dihedral_angle_4_deg 11.711
r_dihedral_angle_3_deg 12.665
r_dihedral_angle_2_deg 37.984
r_dihedral_angle_1_deg 4.228
r_angle_refined_deg 0.853
r_bond_refined_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7028
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 216

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
AMoRE model building
ADSC version: Quantum data collection