3U0L

Crystal structure of the engineered fluorescent protein mRuby, crystal form 1, pH 4.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UISPDB entry 1UIS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52980.1 M Sodium acetate trihydrate pH 4.5, 25% PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9737.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.767α = 90
b = 67.439β = 90
c = 95.063γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2010-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2519.4397.85729756036
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.3295.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1UIS1.2519.035454553121285597.390.127420.127420.125630.16083RANDOM13.485
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.02-0.040.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.3
r_sphericity_free26.256
r_dihedral_angle_4_deg20.115
r_dihedral_angle_3_deg13.145
r_sphericity_bonded9.526
r_dihedral_angle_1_deg7.394
r_rigid_bond_restr7.164
r_angle_refined_deg2.528
r_angle_other_deg1.386
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.3
r_sphericity_free26.256
r_dihedral_angle_4_deg20.115
r_dihedral_angle_3_deg13.145
r_sphericity_bonded9.526
r_dihedral_angle_1_deg7.394
r_rigid_bond_restr7.164
r_angle_refined_deg2.528
r_angle_other_deg1.386
r_chiral_restr0.139
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.008
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1719
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms4

Software

Software
Software NamePurpose
SPECdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling