3IK2 | pdb_00003ik2

Crystal Structure of a Glycoside Hydrolase Family 44 Endoglucanase produced by Clostridium acetobutylium ATCC 824

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E4T	2E4T.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	296	0.2 M (NH4)2SO4, 0.1 M NaOAc, 10% (w/v) PEG 3,350, pH 5.4, vapor diffusion, hanging drop, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.078	α = 90
b = 87.285	β = 90
c = 103.288	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	RIGAKU RAXIS IV++		2007-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.2	66.67	99.5	0.086	11.4	4.87	25388	25388	5	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	2.2	2.28	94.3		0.209	5	4.19	2363

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2E4T.pdb	2.2	66.67	2	5	25388	25324	1260	99.27	0.166	0.155	0.151	0.238	0.2563	RANDOM	13.764

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]
-1.4			0.95		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.773
r_dihedral_angle_4_deg	15.953
r_dihedral_angle_3_deg	14.826
r_dihedral_angle_1_deg	6.404
r_scangle_it	2.932
r_scbond_it	1.999
r_angle_refined_deg	1.446
r_mcangle_it	1.172
r_mcbond_it	0.706
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.176
r_metal_ion_refined	0.115
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4019
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	77

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
AMoRE	phasing