X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details ammonium sulfate, potassium/sodium tartrate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.5 α = 90
b = 121.5 β = 90
c = 29.08 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Charles Supper Double Mirror X-ray Focusing System 2000-07-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.1 45 99.7 0.075 -- -- 10.4 10540 10540 0.0 -3.0 --
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)
2.103 2.18 98.5 0.36 -- 4.2 -- --

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, Based on another structure of a mutant of MLC1P bound to IQ4 that crystallized in a different space group and was determined in the lab by the se-met mad method 2.103 40.0 -- 0.0 10035 10035 504 99.2 -- 0.2013 0.19901 0.23895 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 2.103 2.157 685 36 685 0.258 0.286 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model overall anisotropic
Mean Isotropic B 36.784
Anisotropic B[1][1] -0.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 7.574
r_scbond_it 4.446
r_bond_refined_d 0.022
r_angle_refined_deg 1.817
r_dihedral_angle_1_deg 3.993
r_dihedral_angle_3_deg 13.496
r_chiral_restr 0.141
r_gen_planes_refined 0.009
r_nbd_refined 0.227
r_xyhbond_nbd_refined 0.183
r_symmetry_vdw_refined 0.226
r_symmetry_hbond_refined 0.149
r_mcbond_it 1.542
r_mcangle_it 2.933
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1364
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 81

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALEPACK data reduction
HKL-2000 data collection