X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG 4000, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36 α = 90
b = 69.23 β = 92.96
c = 69.11 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-03-02
CCD ADSC QUANTUM 4 -- 2001-11-16
CCD ADSC QUANTUM 4 -- 2001-12-06
CCD ADSC QUANTUM 4 -- 2001-06-30
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Si(311), Si(111) MAD
Double crystal, Si(111) or Si(311) MAD
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 1.076 MAX II I711
SYNCHROTRON ESRF BEAMLINE ID29 0.9798, 0.9801 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9798, 0.9801 ESRF ID14-4
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2

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
1.7 20 90.5 0.077 -- -- 3.3 34122 34122 0.0 0.0 20.3
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)
1.7 1.75 69.5 0.791 -- 1.6 -- 2587

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 1.7 20.0 -- 0.0 34122 32386 1711 91.0 0.201 0.201 0.198 0.244 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 1.7 1.74 1857 82 1857 0.303 0.365 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.07
Anisotropic B[1][1] 0.98
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.37
Anisotropic B[2][2] -1.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.9
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.621
r_scbond_it 3.034
r_mcangle_it 2.171
r_mcbond_it 1.324
r_symmetry_hbond_refined 0.217
r_symmetry_vdw_other 0.343
r_symmetry_vdw_refined 0.263
r_bond_refined_d 0.027
r_bond_other_d 0.003
r_angle_refined_deg 2.218
r_angle_other_deg 0.984
r_dihedral_angle_1_deg 7.518
r_chiral_restr 0.15
r_gen_planes_refined 0.01
r_gen_planes_other 0.003
r_nbd_refined 0.255
r_nbd_other 0.257
r_nbtor_other 0.095
r_xyhbond_nbd_refined 0.143
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.124
Luzzati ESD (R-Free Set) 0.125
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2473
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 138

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
SHARP model building
SCALA data reduction
MOSFLM data collection