X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 2.1 MALONATE PH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.13 α = 90
b = 83.13 β = 90
c = 180.66 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 2003-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR571 -- -- --

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
2.33 20 99.7 0.066 -- -- 6.96 -- 193519 -- 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)
2.33 2.41 100.0 0.165 -- 11.8 6.84 --

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 2.33 74.54 -- -- -- 26420 1391 99.6 -- 0.171 0.168 0.22 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 2.33 2.39 -- 97 1933 0.154 0.255 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.94
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.8
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.119
r_scbond_it 2.575
r_mcangle_it 1.685
r_mcbond_it 0.934
r_nbd_refined 0.206
r_gen_planes_other 0.005
r_gen_planes_refined 0.008
r_chiral_restr 0.102
r_dihedral_angle_1_deg 6.628
r_angle_other_deg 0.872
r_angle_refined_deg 1.742
r_bond_other_d 0.002
r_bond_refined_d 0.024
r_nbd_other 0.253
r_nbtor_other 0.088
r_xyhbond_nbd_refined 0.188
r_symmetry_vdw_refined 0.263
r_symmetry_vdw_other 0.254
r_symmetry_hbond_refined 0.116
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4048
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 389

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK 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