4G25

Crystal Structure of proteinaceous RNase P 1 (PRORP1) from A. thaliana, SeMet substituted form with Sr


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G23PDB ENTRY 4G23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.527718% PEG 3,350, 0.1 M sodium citrate pH 5.5, and 0.02 M SrCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8657.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.844α = 90
b = 111.814β = 90
c = 140.226γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2012-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.968APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
125098.40.08412.65.44550144773
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0797.90.632.65.44456

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4G23233.54473342464226998.40.196060.194050.23354RANDOM44.137
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]
0.171.6-1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.483
r_dihedral_angle_4_deg21.697
r_dihedral_angle_3_deg14.589
r_dihedral_angle_1_deg6.119
r_angle_refined_deg1.552
r_angle_other_deg1.128
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.483
r_dihedral_angle_4_deg21.697
r_dihedral_angle_3_deg14.589
r_dihedral_angle_1_deg6.119
r_angle_refined_deg1.552
r_angle_other_deg1.128
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3787
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms2

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling