4PQ9 | pdb_00004pq9

Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RQ0	pdb entry 3rq0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	MCSG1(a7): 25% PEG3350, Bis-Tris:HCl, pH=5.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.73	28.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.12	α = 109.45
b = 46.84	β = 95.63
c = 51.84	γ = 99.79

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	CCD	MARMOSAIC 225 mm CCD	Beryllium Lenses	2014-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97857	APS	21-ID-F

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	1.2	50	94.3	0.032	26.2	3.9	121825	114838		-3	12.164

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	1.2	1.23	91.3		0.131	9.54

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 (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 3rq0	1.2	48.2	120457	114838	5619	94.38	0.1189	0.1176	0.1178	0.1435	0.1433	RANDOM	10.217

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]
0.32	0.08	0.19	-0.24		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_sphericity_free	29.896
r_dihedral_angle_4_deg	16.585
r_dihedral_angle_3_deg	11.796
r_sphericity_bonded	7.61
r_dihedral_angle_1_deg	7.122
r_rigid_bond_restr	1.655
r_mcangle_it	1.613
r_angle_refined_deg	1.57
r_mcbond_it	1.222
r_mcbond_other	1.222
r_angle_other_deg	0.804
r_chiral_restr	0.102
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3696
Nucleic Acid Atoms
Solvent Atoms	558
Heterogen Atoms	35

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing