X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 10.5
Temperature 293.0
Details 30% PEG-400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.51 α = 90
b = 52.51 β = 90
c = 34.71 γ = 120
Symmetry
Space Group P 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APS water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2002-10-25
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97944, 0.97924, 0.95658 APS 19-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
1.95 45.48 100.0 -- 0.068 -- 7.49 -- 7337 -- -- 41.58
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)
1.95 2.02 70.02 -- 0.245 3.7 3.99 563

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
MAD 1.95 45.48 -- -- -- 6993 339 93.94 -- 0.15907 0.15603 0.22061 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 1.95 2.002 -- 19 356 0.225 0.321 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 39.27
Anisotropic B[1][1] -2.39
Anisotropic B[1][2] -1.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.59
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.609
r_dihedral_angle_4_deg 23.559
r_scbond_it 5.692
r_dihedral_angle_1_deg 6.361
r_scangle_it 7.133
r_xyhbond_nbd_refined 0.239
r_angle_refined_deg 1.441
r_mcbond_it 2.511
r_symmetry_vdw_refined 0.148
r_bond_other_d 0.002
r_dihedral_angle_2_deg 39.307
r_symmetry_hbond_refined 0.232
r_gen_planes_refined 0.007
r_chiral_restr 0.097
r_bond_refined_d 0.018
r_symmetry_vdw_other 0.214
r_nbd_refined 0.206
r_mcangle_it 3.116
r_gen_planes_other 0.001
r_nbtor_other 0.089
r_angle_other_deg 0.804
r_nbd_other 0.193
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 890
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 74

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
REFMAC 5.1.9999 Structure Refinement
Software
Software Name Purpose
RESOLVE model building
SOLVE model building
REFMAC version: 5.1.9999 refinement
DENZO data collection
SCALEPACK data reduction