X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 296.0
Details 2.2 M sodium malonate (pH 7.0)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 131.82 α = 90
b = 53.29 β = 90
c = 53.74 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-11-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00002 PAL/PLS 5C (4A)

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
2.1 50 99.5 -- -- -- 5.6 -- 22810 -- -- --
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)
2.1 2.14 100.0 0.591 -- 3.6 5.6 --

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 2.1 30.0 -- -- -- 21608 1113 99.46 -- 0.21237 0.2109 0.24247 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 2.1 2.154 -- 95 1553 0.276 0.298 -- 99.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.293
Anisotropic B[1][1] -1.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.61
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 13.878
r_angle_refined_deg 1.482
r_chiral_restr 0.076
r_bond_other_d 0.005
r_scbond_other 3.963
r_scangle_other 6.534
r_dihedral_angle_2_deg 31.378
r_angle_other_deg 1.233
r_gen_planes_other 0.002
r_mcangle_other 5.055
r_dihedral_angle_1_deg 4.855
r_mcangle_it 5.056
r_dihedral_angle_4_deg 19.429
r_mcbond_it 3.321
r_gen_planes_refined 0.005
r_mcbond_other 3.321
r_bond_refined_d 0.01
r_long_range_B_other 9.809
r_long_range_B_refined 9.851
r_scbond_it 3.965
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2245
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 108

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0103
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing