X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.1 M magnesium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.99 α = 90
b = 129.2 β = 90
c = 36.85 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 MARMOSAIC 225 mm CCD -- 2006-03-16
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.9793 APS 22-BM

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
1.79 50 95.7 0.081 -- -- 3.2 23548 23518 -6.0 -3.0 25.8
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)
1.8 1.86 78.1 0.44 -- 2.19 3.0 1897

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
SAD 1.79 50.0 -- 0.0 23473 22273 1200 95.47 0.214 0.214 0.212 0.255 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 1.792 1.839 -- 67 1249 0.266 0.312 -- 72.79
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 34.596
Anisotropic B[1][1] 3.99
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.45
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 6.155
r_scbond_it 4.328
r_mcangle_it 4.269
r_mcbond_it 3.374
r_symmetry_hbond_refined 0.122
r_bond_refined_d 0.016
r_angle_refined_deg 1.505
r_dihedral_angle_1_deg 4.586
r_dihedral_angle_2_deg 36.524
r_dihedral_angle_3_deg 16.695
r_dihedral_angle_4_deg 21.261
r_chiral_restr 0.104
r_gen_planes_refined 0.006
r_nbd_refined 0.216
r_nbtor_refined 0.302
r_xyhbond_nbd_refined 0.156
r_symmetry_vdw_refined 0.185
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1966
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 147

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement