4IPM | pdb_00004ipm

Crystal structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with thiocellobiose

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	289	100mM sodium acetate pH 4.5, 500mM CaCl2, 15% (w/v) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.49	α = 90
b = 79.78	β = 90
c = 105.16	γ = 90

Symmetry
Space Group	P 2 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	CCD	ADSC QUANTUM 315r		2012-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.14	63.559	96.4	0.084	8.4	3.7	150535	140362

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.14	1.16	72.7		0.636	0.482	1.3	2.3	5172

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	4GWA	1.14	23	150535	140221	7047	96.07	0.1234	0.1217	0.12	0.1551	0.16	RANDOM	12.7332

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]
0.02			-0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	59.449
r_dihedral_angle_2_deg	32.308
r_dihedral_angle_4_deg	22.078
r_sphericity_bonded	16.264
r_dihedral_angle_3_deg	12.036
r_dihedral_angle_1_deg	6.595
r_rigid_bond_restr	6.196
r_angle_refined_deg	2.025
r_angle_other_deg	0.958
r_chiral_restr	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	59.449
r_dihedral_angle_2_deg	32.308
r_dihedral_angle_4_deg	22.078
r_sphericity_bonded	16.264
r_dihedral_angle_3_deg	12.036
r_dihedral_angle_1_deg	6.595
r_rigid_bond_restr	6.196
r_angle_refined_deg	2.025
r_angle_other_deg	0.958
r_chiral_restr	0.138
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3258
Nucleic Acid Atoms
Solvent Atoms	687
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.