X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details sodium formate, MES buffer, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.05 α = 90
b = 56.9 β = 130.51
c = 104.98 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-04-26
Diffraction Radiation
Monochromator Protocol
Si 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9A .9792 NSLS X9A

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 35 98.3 -- 0.083 -- 2.2 84266 82833 -3.0 -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)
2.0 2.07 92.3 -- 0.359 3.6 3.0 4296

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 2.0 30.0 -- -3.0 -- 40441 2134 100.0 0.1987 0.19879 0.19705 0.23149 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 2.0 2.052 -- 165 2975 0.3 0.307 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.358
Anisotropic B[1][1] 0.8
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.1
Anisotropic B[2][2] -0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.91
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.766
r_scbond_it 2.884
r_mcangle_it 1.622
r_mcbond_it 0.845
r_symmetry_hbond_other 0.009
r_symmetry_hbond_refined 0.186
r_symmetry_vdw_other 0.319
r_symmetry_vdw_refined 0.201
r_xyhbond_nbd_other 0.331
r_xyhbond_nbd_refined 0.221
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.484
r_angle_other_deg 1.125
r_dihedral_angle_1_deg 4.159
r_dihedral_angle_3_deg 16.498
r_chiral_restr 0.08
r_gen_planes_refined 0.008
r_gen_planes_other 0.007
r_nbd_refined 0.257
r_nbd_other 0.227
r_nbtor_other 0.335
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3808
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 175

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement