3RCL

Human Cyclophilin D Complexed with a Fragment


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.3
Temperature 291.0
Details 30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.06 α = 90
b = 57.06 β = 90
c = 87.46 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
AREA DETECTOR MARRESEARCH -- 2008-02-23
Diffraction Radiation
Monochromator Protocol
yale mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
1.7 22 98.1 -- 0.02 -- 5.9 15630 15333 -- 5.9 --
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)
1.7 1.749 87.4 -- 0.037 3.7 3.7 --

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 1.7 21.86 -- -- 15630 15333 799 98.49 -- 0.13363 0.13181 0.16936 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 1.705 1.749 -- 48 894 0.185 0.24 -- 79.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 5.838
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.12
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_mcbond_other 0.056
r_gen_planes_other 0.001
r_angle_other_deg 0.891
r_chiral_restr 0.065
r_mcbond_it 0.264
r_gen_planes_refined 0.003
r_mcangle_it 0.477
r_bond_refined_d 0.006
r_scbond_it 0.76
r_dihedral_angle_2_deg 31.977
r_dihedral_angle_4_deg 21.177
r_angle_refined_deg 1.043
r_scangle_it 1.275
r_dihedral_angle_3_deg 12.272
r_dihedral_angle_1_deg 5.925
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1240
Nucleic Acid Atoms 0
Heterogen Atoms 34
Solvent Atoms 356

Software

Software
Software Name Purpose
MAR345dtb data collection
X-PLOR model building
REFMAC refinement version: 5.4.0062
MOSFLM data reduction
SCALA data scaling
X-PLOR phasing