4GZJ

Active-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose and laminaratetrose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GZI	PDB ENTRY 4GZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	292	0.1 M sodium citrate, 0.2 M ammonium acetate, 24% PEG 8000, 0.4 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.307	α = 90
b = 49.202	β = 98.84
c = 57.431	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	IMAGE PLATE	MAR555 FLAT PANEL	mirrors	2007-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81480	EMBL/DESY, HAMBURG	X11

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	1.55	40	100	0.091	15.3	3.8	44391	44391		-3	21.2

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	1.55	1.61	100		0.68	2.1	3.8	4390

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	R-FREE	PDB ENTRY 4GZI	1.55	20	-3	43213	43213	1139	99.91	0.1515	0.1515	0.1507	0.1806	RANDOM	15.27

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]
-0.01		-0.47	-0.49		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.661
r_dihedral_angle_4_deg	15.502
r_dihedral_angle_3_deg	11.925
r_dihedral_angle_1_deg	6.2
r_scangle_it	3.674
r_scbond_it	2.47
r_angle_refined_deg	1.644
r_mcangle_it	1.592
r_mcbond_it	1.051
r_angle_other_deg	0.887
r_mcbond_other	0.32
r_nbd_refined	0.218
r_symmetry_vdw_other	0.195
r_nbtor_refined	0.19
r_nbd_other	0.173
r_symmetry_vdw_refined	0.134
r_symmetry_hbond_refined	0.125
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.11
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2509
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	57

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling