8B2G

SH3-like domain from Penicillium virgatum muramidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8B2S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PACT C9=0.2 M LiCl, 0.1 M Hepes pH 7.0, 20% PEG 6K, MMS (microseed matrix screening) from JCSG, C7=0.2 M zinc acetate dehydrate, 0.1 M sodium acetate, 10%w/v PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.142	α = 90
b = 59.824	β = 112.131
c = 36.109	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2017-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.28249	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	1.5	59.82	93.8	0.082	0.108	0.069	0.995	7.4	4		21381

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	1.5	1.53	66.8		0.967	1.282	0.835	0.261	1	3.2

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	FREE R-VALUE	8B2S	1.5	33.479	21359	1052	93.218	0.164	0.1631	0.17	0.1725	0.18	16.849

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]
-3.759		2.023	3.359		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.335
r_dihedral_angle_3_deg	9.558
r_dihedral_angle_1_deg	6.603
r_lrange_it	4.768
r_lrange_other	4.707
r_scangle_it	3.895
r_scangle_other	3.893
r_mcangle_other	2.885
r_mcangle_it	2.867
r_scbond_it	2.735
r_scbond_other	2.733
r_mcbond_other	1.998
r_mcbond_it	1.997
r_angle_refined_deg	1.795
r_dihedral_angle_2_deg	1.717
r_angle_other_deg	0.565
r_nbd_refined	0.212
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.176
r_nbd_other	0.118
r_xyhbond_nbd_refined	0.103
r_ncsr_local_group_1	0.093
r_metal_ion_refined	0.085
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.082
r_symmetry_nbd_refined	0.031
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1085
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	17

Software

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