Experiment: 4KRU

X-ray structure of catalytic domain of endolysin from clostridium perfringens phage phiSM101

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JFX	PDB ENTRY 1JFX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	20% PEG 3000, 0.2M Lithium sulphate, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.77	α = 90
b = 57.62	β = 90
c = 73.42	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS VII	mirrors (VariMax Optic)	2012-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.37	30.96	98.4	0.024	42.5	6.15	42675	42675			10.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.37	1.42	85		0.071	11.7	2.52	3633

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JFX	1.37	30.96	42613	42613	2141	98.2	0.173	0.172	0.172	0.1705	0.193	0.1913	RANDOM	12.9

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]
0.81			-0.35		-0.46

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.2
c_scangle_it	2.39
c_scbond_it	1.64
c_angle_deg	1.4
c_mcangle_it	1.22
c_mcbond_it	0.82
c_improper_angle_d	0.67
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1710
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	35

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling