6ZMV

Structure of muramidase from Trichobolus zukalii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X8R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	lithium sulphate, ammonium sulphate, sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.398	α = 97.076
b = 48.582	β = 99.531
c = 55.737	γ = 98.15

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.98	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.4	27.187	93.8	0.992	15.8	2.1		73721

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.436			0.956

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2X8R	1.4	27.17	73721	3758	93.765	0.106	0.1041	0.1427	9.194

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]
-0.098	0.097	-0.075	0.391	-0.217	-0.206

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.957
r_dihedral_angle_4_deg	11.325
r_dihedral_angle_3_deg	10.961
r_dihedral_angle_1_deg	6.899
r_lrange_it	4.577
r_lrange_other	3.358
r_scangle_it	2.717
r_scangle_other	2.637
r_rigid_bond_restr	2.609
r_scbond_it	2.236
r_scbond_other	2.187
r_angle_refined_deg	1.909
r_angle_other_deg	1.744
r_mcangle_it	1.727
r_mcangle_other	1.727
r_mcbond_it	1.387
r_mcbond_other	1.387
r_symmetry_nbd_refined	0.309
r_xyhbond_nbd_refined	0.298
r_nbd_refined	0.245
r_nbd_other	0.24
r_symmetry_xyhbond_nbd_refined	0.205
r_nbtor_refined	0.196
r_symmetry_nbd_other	0.19
r_chiral_restr	0.115
r_symmetry_nbtor_other	0.091
r_ncsr_local_group_1	0.071
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3167
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing