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_angle_refined_deg 2.06
r_nbd_other 0.266
r_nbd_refined 0.199
r_dihedral_angle_1_deg 7.204
r_symmetry_hbond_refined 0.147
r_nbtor_other 0.093
r_gen_planes_refined 0.01
r_xyhbond_nbd_refined 0.155
r_angle_other_deg 0.954
r_mcangle_it 2.264
r_chiral_restr 0.136
r_gen_planes_other 0.005
r_symmetry_vdw_refined 0.241
r_scangle_it 5.602
r_symmetry_vdw_other 0.289
r_mcbond_it 1.31
r_scbond_it 3.522
r_bond_other_d 0.002
r_bond_refined_d 0.027
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 3692
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 290

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
AMoRE phasing
REFMAC refinement version: 5.1.19
CCP4 data scaling version: (SCALA)