X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 200MM CALCIUM ACETATE IN 100MM HEPES BUFFER AT PH 7.0. PRECIPITANT WAS 18% POLYETHYLENE GLYCOL 8000.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.5 α = 90
b = 60.15 β = 90
c = 97.21 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
IMAGE PLATE MARRESEARCH -- 1999-10-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
1.5 20 99.5 0.07 -- -- 3.7 -- 54127 -- 0.0 --
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)
1.5 1.55 95.0 0.358 -- 3.4 3.5 --

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
OTHER 1.5 20.0 -- -- -- 51648 2710 99.4 -- 0.115 0.113 0.149 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 1.5 1.54 -- 175 3475 0.144 0.182 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.34
Anisotropic B[1][1] -0.42
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.609
r_scbond_it 2.489
r_mcangle_it 1.759
r_mcbond_it 1.205
r_nbd_refined 0.225
r_gen_planes_other 0.003
r_gen_planes_refined 0.009
r_chiral_restr 0.108
r_dihedral_angle_4_deg 19.858
r_dihedral_angle_3_deg 11.815
r_dihedral_angle_2_deg 40.135
r_dihedral_angle_1_deg 5.674
r_angle_other_deg 1.357
r_angle_refined_deg 1.704
r_bond_other_d 0.002
r_bond_refined_d 0.015
r_nbd_other 0.275
r_nbtor_other 0.082
r_xyhbond_nbd_refined 0.134
r_metal_ion_refined 0.137
r_symmetry_vdw_refined 0.129
r_symmetry_vdw_other 0.229
r_symmetry_hbond_refined 0.127
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2839
Nucleic Acid Atoms 0
Heterogen Atoms 57
Solvent Atoms 465

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.06 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.06 refinement