9FBS | pdb_00009fbs

Deletion mutant of chitinase MmChi60

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4W5Z	similar content

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	20% (w/v) PEG 4000, 0.4 M MgCl2, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.764	α = 90
b = 74.009	β = 90
c = 172.538	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS3 2M	focusing mirrors	2017-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.35	50	99.3	0.144	0.152	0.997	12.7	9.4		13787

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.5	96		0.961	1.015	0.762	2.24	9.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.354	43.134	13786	828	99.266	0.191	0.1859	0.1979	0.2655	0.2735	42.173

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]
-0.131			-0.018		0.149

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.897
r_dihedral_angle_3_deg	14.927
r_lrange_it	7.379
r_lrange_other	7.376
r_dihedral_angle_1_deg	6.596
r_scangle_it	5.736
r_scangle_other	5.735
r_mcangle_it	4.671
r_mcangle_other	4.671
r_dihedral_angle_2_deg	3.947
r_scbond_it	3.732
r_scbond_other	3.731
r_mcbond_it	3.148
r_mcbond_other	3.148
r_angle_refined_deg	1.356
r_angle_other_deg	0.496
r_nbd_refined	0.22
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.16
r_nbd_other	0.147
r_symmetry_xyhbond_nbd_refined	0.143
r_xyhbond_nbd_refined	0.117
r_metal_ion_refined	0.077
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2551
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing