X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 283.0
Details 0.1M Hepes, 1.1M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.51 α = 90
b = 58.51 β = 90
c = 108.58 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-07-09
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 1.278 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
2.27 50.67 100.0 -- 0.091 -- 19.0 9797 9797 2.0 2.0 --
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)
2.27 2.39 100.0 0.308 0.308 2.5 17.9 1415

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 2.27 50.67 -- 0.0 9776 9756 706 99.98 -- 0.1751 0.1716 0.219 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 2.271 2.329 -- 43 683 0.2 0.275 -- 99.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.9541
Anisotropic B[1][1] -4.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.29
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_chiral_restr 0.082
r_dihedral_angle_4_deg 16.563
r_dihedral_angle_3_deg 15.709
r_dihedral_angle_2_deg 41.427
r_dihedral_angle_1_deg 6.247
r_angle_refined_deg 1.195
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1596
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 25

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
MOLREP molecular replacement
SCALA version: 3.3.20 data reduction
Mosflm data collection