3UR8 | pdb_00003ur8

Lower-density crystal structure of potato endo-1,3-beta-glucanase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UR7	PDB ENTRY 3UR7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	292	0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.361	α = 90
b = 49.056	β = 103.56
c = 82.618	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	0.8148	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	1.26	40	95.4	0.059	19.2	4.6	151662	151662		-3	12.9

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	1.26	1.31	93.8		0.467	2	3.3	14787

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 (All)	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	R free	PDB ENTRY 3UR7	1.26	19.54	149903	149903	1654	95.04	0.14277	0.14277	0.14235	0.14	0.18244	0.18	RANDOM	9.348

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		-0.01	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.975
r_dihedral_angle_4_deg	15.339
r_dihedral_angle_3_deg	11.999
r_sphericity_free	10.821
r_dihedral_angle_1_deg	6.297
r_sphericity_bonded	5.096
r_scangle_it	4.627
r_scbond_it	3.554
r_mcangle_it	2.493
r_mcbond_it	2.097
r_rigid_bond_restr	1.807
r_angle_refined_deg	1.744
r_angle_other_deg	1.044
r_mcbond_other	0.933
r_symmetry_vdw_other	0.264
r_nbd_refined	0.22
r_nbtor_refined	0.191
r_nbd_other	0.173
r_symmetry_vdw_refined	0.156
r_chiral_restr	0.119
r_xyhbond_nbd_refined	0.111
r_symmetry_hbond_refined	0.111
r_nbtor_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5091
Nucleic Acid Atoms
Solvent Atoms	763
Heterogen Atoms

Software

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