X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details PROTEIN 16 MG/ML, AMMONIUM SULFATE 2.0 M, SODIUM ACETATE 100 mM, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.2 α = 90
b = 120.2 β = 90
c = 177.34 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-11-08
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.937 ESRF ID14-1

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
1.9 51.3 95.5 0.083 0.083 -- 5.0 57308 57308 0.0 0.0 29.5
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)
1.9 2.0 70.0 0.324 0.324 2.1 2.1 5977

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 1.95 20.0 0.0 0.0 52296 52296 2762 99.03 0.17259 0.17259 0.17146 0.19412 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 1.95 2.0 -- 181 3455 0.216 0.225 -- 90.27
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.658
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.16
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 18.639
r_scbond_it 3.052
r_chiral_restr 0.131
r_dihedral_angle_1_deg 7.444
r_symmetry_vdw_refined 0.127
r_gen_planes_refined 0.008
r_mcbond_other 0.31
r_angle_other_deg 1.369
r_nbd_other 0.216
r_nbtor_refined 0.167
r_nbtor_other 0.113
r_gen_planes_other 0.001
r_nbd_refined 0.205
r_mcangle_it 1.696
r_bond_refined_d 0.021
r_angle_refined_deg 1.907
r_xyhbond_nbd_refined 0.156
r_bond_other_d 0.003
r_symmetry_vdw_other 0.393
r_dihedral_angle_2_deg 36.937
r_scangle_it 4.648
r_dihedral_angle_3_deg 12.748
r_symmetry_hbond_refined 0.199
r_mcbond_it 1.323
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1980
Nucleic Acid Atoms 0
Heterogen Atoms 209
Solvent Atoms 335

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DNA data collection
MOSFLM data reduction
SCALA data scaling
MOLREP phasing