X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 294.0
Details CITRATE BUFFER, AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.78 α = 90
b = 29.43 β = 115.72
c = 40.1 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 Double crystal focusing mirrors 2002-05-29
Diffraction Radiation
Monochromator Protocol
SI (III) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.9795,0.9791,0.9718 NSLS X9B

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
1.6 22.82 84.6 0.038 -- -- -- -- 9312 -- -3.0 --
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)
1.6 1.66 35.9 0.21 0.032 -- -- --

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 1.6 10.0 -- -- 9312 9256 838 98.61 -- 0.13212 0.12745 0.18046 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 1.6 1.64 -- 24 238 0.204 0.328 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.464
Anisotropic B[1][1] 2.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.6
Anisotropic B[2][2] -0.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.12
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 1.841
r_rigid_bond_restr 1.497
r_scangle_it 3.74
r_scbond_it 2.418
r_mcangle_it 2.142
r_mcbond_it 1.259
r_symmetry_hbond_refined 0.209
r_symmetry_vdw_other 0.298
r_symmetry_vdw_refined 0.204
r_bond_refined_d 0.016
r_bond_other_d 0.006
r_angle_refined_deg 1.509
r_angle_other_deg 0.883
r_dihedral_angle_1_deg 5.801
r_chiral_restr 0.104
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_nbd_refined 0.243
r_nbd_other 0.266
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.208
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 855
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 134

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHELXS Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SHELXS model building
SCALEPACK data reduction
DENZO data collection