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 Experiment
ID # Data Collection Temperature
1 100
2 100
3 100
4 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-30
CCD MARRESEARCH -- 2002-03-02
CCD ADSC QUANTUM 4 -- 2001-12-06
CCD ADSC QUANTUM 4 -- 2001-11-16
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Si(111) SINGLE WAVELENGTH
Si(311), Si(111) MAD
Double crystal, Si(111) or Si(311) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9798, 0.9801 ESRF ID29
SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9798, 0.9801 ESRF ID14-4
SYNCHROTRON MAX II BEAMLINE I711 1.076 MAX_II I711

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_angle_refined_deg 2.218
r_mcangle_it 2.171
r_scangle_it 4.621
r_mcbond_it 1.324
r_nbd_refined 0.255
r_symmetry_vdw_refined 0.263
r_bond_other_d 0.003
r_angle_other_deg 0.984
r_dihedral_angle_1_deg 7.518
r_nbd_other 0.257
r_xyhbond_nbd_refined 0.143
r_symmetry_vdw_other 0.343
r_gen_planes_other 0.003
r_nbtor_other 0.095
r_bond_refined_d 0.027
r_symmetry_hbond_refined 0.217
r_gen_planes_refined 0.01
r_chiral_restr 0.15
r_scbond_it 3.034
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 2512
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 138

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
SHARP phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)