X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.25 α = 90
b = 122.25 β = 90
c = 155.52 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD BERYLLIUM LENSES 2009-10-16
Diffraction Radiation
Monochromator Protocol
DIAMOND [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.05 50 97.5 0.079 0.079 -- 7.2 37125 36107 0.0 -3.0 25.6
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)
2.05 2.09 96.2 0.634 0.634 2.543 6.2 --

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 2.052 50.0 -- 0.0 -- 36106 1811 97.27 -- 0.165 0.163 0.196 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 2.052 2.105 -- 133 2437 0.202 0.255 -- 94.17
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.735
Anisotropic B[1][1] -0.44
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.89
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.182
r_scbond_it 3.074
r_mcangle_it 1.813
r_mcbond_other 0.0
r_bond_refined_d 0.02
r_bond_other_d 0.0
r_angle_refined_deg 1.767
r_angle_other_deg 4.18
r_dihedral_angle_1_deg 6.121
r_dihedral_angle_2_deg 36.447
r_dihedral_angle_3_deg 14.525
r_dihedral_angle_4_deg 17.812
r_chiral_restr 0.101
r_gen_planes_refined 0.007
r_gen_planes_other 0.008
r_mcbond_it 0.992
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3778
Nucleic Acid Atoms 0
Heterogen Atoms 154
Solvent Atoms 163

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000: MOLREP Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 version: 5.5.0109 refinement