X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 297.0
Details PEG 6000, NaCl, MgCl2, HEPES, ADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.9 α = 90
b = 92.4 β = 90
c = 261.59 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2002-03-03
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 0.9330 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
2.6 30 98.7 0.124 0.124 -- 3.5 66737 66708 1.0 1.1 57.1
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)
2.6 2.74 98.7 0.657 0.657 1.1 3.5 9717

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 2.6 20.0 0.0 0.0 67769 65273 1283 98.21 0.21565 0.21565 0.21497 0.24892 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 2.6 2.666 -- 86 4770 0.338 0.42 -- 98.94
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS
Mean Isotropic B 10.362
Anisotropic B[1][1] -4.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.47
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.082
r_nbd_other 0.21
r_nbd_refined 0.182
r_gen_planes_other 0.008
r_gen_planes_refined 0.004
r_chiral_restr 0.06
r_dihedral_angle_1_deg 5.82
r_angle_other_deg 0.792
r_angle_refined_deg 1.133
r_bond_other_d 0.003
r_bond_refined_d 0.009
r_xyhbond_nbd_refined 0.193
r_symmetry_vdw_refined 0.126
r_symmetry_vdw_other 0.236
r_symmetry_hbond_refined 0.146
r_mcbond_it 0.273
r_mcangle_it 0.523
r_scbond_it 0.995
r_scangle_it 1.381
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12286
Nucleic Acid Atoms 714
Heterogen Atoms 56
Solvent Atoms 364

Software

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