X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.8
Temperature 293.0
Details 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.5 α = 90
b = 111.5 β = 90
c = 56.53 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2003-02-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.993 ESRF ID14-2

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
2.75 35 99.9 -- 0.056 -- 5.1 10793 10782 -- -- 97.65
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)
2.75 2.9 99.7 -- 0.508 2.7 4.8 1551

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 2.75 32.21 -- 0.0 10128 10118 656 99.9 0.21173 0.21173 0.20792 0.27069 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 2.75 2.821 -- 48 735 0.357 0.449 -- 99.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 77.147
Anisotropic B[1][1] 0.34
Anisotropic B[1][2] 0.17
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.51
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.503
r_scbond_it 2.441
r_mcangle_it 1.535
r_mcbond_it 1.19
r_symmetry_hbond_refined 0.316
r_bond_refined_d 0.015
r_angle_refined_deg 1.779
r_dihedral_angle_1_deg 7.293
r_dihedral_angle_2_deg 34.274
r_dihedral_angle_3_deg 19.162
r_dihedral_angle_4_deg 19.232
r_chiral_restr 0.114
r_gen_planes_refined 0.006
r_nbd_refined 0.227
r_nbtor_refined 0.314
r_xyhbond_nbd_refined 0.179
r_symmetry_vdw_refined 0.215
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2022
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 9

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2 refinement
AMoRE model building
ADSC version: Quantum data collection