X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.5
Details 8.5 % PEG 8K, 0.1 M NA-ACETATE PH 5.5, 0.01 MM ZNCL2, 5 MM NADPH

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 189.31 α = 90
b = 189.31 β = 90
c = 98.65 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC -- 2002-06-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- 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
2.6 43.7 100.0 0.05 -- -- 6.1 -- 62012 -- -- --
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 2.67 100.0 0.192 -- 3.9 5.9 --

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 2.6 158.11 -- -- -- 58842 3140 100.0 -- 0.173 0.171 0.202 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 2.67 -- 254 4318 0.208 0.256 -- --
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.31
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.19
r_gen_planes_other 0.003
r_gen_planes_refined 0.004
r_chiral_restr 0.067
r_dihedral_angle_1_deg 5.897
r_angle_other_deg 0.776
r_angle_refined_deg 1.226
r_bond_other_d 0.002
r_bond_refined_d 0.01
r_nbd_other 0.231
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.168
r_symmetry_vdw_refined 0.172
r_symmetry_vdw_other 0.254
r_symmetry_hbond_refined 0.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9752
Nucleic Acid Atoms 0
Heterogen Atoms 192
Solvent Atoms 348

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
MOLREP model building