X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 100 mM Na/H MES, 50 to 60 mM CaCl2, 30% v/v PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.01 α = 90
b = 66.6 β = 114.02
c = 80.78 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 -- 2001-12-23
Diffraction Radiation
Monochromator Protocol
Bent Ge(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.00000 APS 14-BM-C

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
1.85 50 -- 0.056 -- -- 1.92 62043 62043 -- -2.0 --
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)
1.85 1.92 91.7 0.467 -- 1.75 1.84 --

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 1.848 50.0 -- 0.0 62026 58907 3119 93.13 -- 0.19119 0.18839 0.24461 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 1.848 1.896 -- 231 4099 0.254 0.316 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 26.719
Anisotropic B[1][1] -0.88
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.37
Anisotropic B[2][2] 1.67
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.49
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.094
r_nbd_other 0.293
r_nbd_refined 0.26
r_gen_planes_other 0.014
r_gen_planes_refined 0.022
r_chiral_restr 0.109
r_dihedral_angle_2_deg 20.324
r_dihedral_angle_1_deg 8.103
r_angle_other_deg 0.718
r_angle_refined_deg 1.37
r_bond_other_d 0.003
r_bond_refined_d 0.008
r_xyhbond_nbd_refined 0.253
r_xyhbond_nbd_other 0.349
r_symmetry_vdw_refined 0.297
r_symmetry_vdw_other 0.371
r_symmetry_hbond_refined 0.344
r_symmetry_hbond_other 0.605
r_mcbond_it 2.545
r_mcangle_it 3.975
r_scbond_it 6.38
r_scangle_it 9.547
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5688
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 665

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SCALEPACK data reduction
DENZO data collection