X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.9
Temperature 293.0
Details PEG 8000, calcium acetate, cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 178.82 α = 90
b = 69.62 β = 90
c = 45.27 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-09-29
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
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
1.99 87.71 -- 0.086 -- -- 5.4 34536 34536 0.0 0.0 23.9
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)
1.99 2.15 82.0 0.24 -- 3.0 3.4 --

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 1.99 87.71 -- -- 34445 32723 1754 87.28 -- 0.1682 0.16555 0.21634 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 1.995 2.046 -- 114 2159 0.187 0.247 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.994
Anisotropic B[1][1] 0.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.43
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.093
r_nbd_other 0.266
r_nbd_refined 0.199
r_gen_planes_other 0.005
r_gen_planes_refined 0.01
r_chiral_restr 0.136
r_dihedral_angle_1_deg 7.204
r_angle_other_deg 0.954
r_angle_refined_deg 2.06
r_bond_other_d 0.002
r_bond_refined_d 0.027
r_xyhbond_nbd_refined 0.155
r_symmetry_vdw_refined 0.241
r_symmetry_vdw_other 0.289
r_symmetry_hbond_refined 0.147
r_mcbond_it 1.31
r_mcangle_it 2.264
r_scbond_it 3.522
r_scangle_it 5.602
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati ESD (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3626
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 290

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection