8B2S

GH24 family muramidase from Trichophaea saccata with an SH3-like cell wall binding domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	AmSO4 screen (Qiagen), condition C3: 0.2 M potassium fluoride, 2.2 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.438	α = 90
b = 99.438	β = 90
c = 133.254	γ = 120

Symmetry
Space Group	P 31 2 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	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.94	46.582	100	0.073	0.083	0.04	0.999	16.2	8.2		56987			32.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.94	1.99	100		2.263	2.582	1.232	0.328	0.9	8.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1HDE	1.94	46.582	56937	2862	99.981	0.17	0.168	0.18	0.2013	0.21	40.867

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]
0.129	0.064		0.129		-0.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.64
r_dihedral_angle_3_deg	12.278
r_dihedral_angle_2_deg	6.594
r_lrange_it	6.234
r_dihedral_angle_1_deg	6.212
r_lrange_other	6.158
r_scangle_it	4.906
r_scangle_other	4.905
r_scbond_it	4.192
r_scbond_other	4.191
r_mcangle_it	3.222
r_mcangle_other	3.221
r_mcbond_other	2.512
r_mcbond_it	2.511
r_angle_refined_deg	1.54
r_angle_other_deg	0.536
r_metal_ion_refined	0.401
r_nbd_refined	0.206
r_nbd_other	0.204
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbd_refined	0.118
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.073
r_ncsr_local_group_1	0.066
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3610
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XDS	data reduction
xia2	data reduction
Aimless	data scaling
BALBES	phasing
REFMAC	refinement