1Z3W | pdb_00001z3w

Structure of Phanerochaete chrysosporium cellobiohydrolase Cel7D (CBH58) in complex with cellobioimidazole

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GPI	PDB entry 1GPI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	TRIS-HCl, calcium chloride, PEG 5000, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.382	α = 90
b = 46.578	β = 102.58
c = 98.505	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 4	Toroidal mirror	2001-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

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	1.7	43	93.2	0.052	14	2.3	39785	39785

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	1.7	1.79	92.4		0.194	3.8		2685

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	PDB entry 1GPI	1.7	36.27	37334	37334	2350	100	0.18108	0.17824	0.18	0.22729	0.24	RANDOM	17.761

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]
1.27		-0.61	-0.25		-1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.896
r_dihedral_angle_1_deg	6.044
r_scangle_it	5.472
r_mcangle_it	4.842
r_scbond_it	4.323
r_mcbond_it	4.126
r_angle_refined_deg	1.215
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.896
r_dihedral_angle_1_deg	6.044
r_scangle_it	5.472
r_mcangle_it	4.842
r_scbond_it	4.323
r_mcbond_it	4.126
r_angle_refined_deg	1.215
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.086
r_symmetry_hbond_refined	0.049
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3198
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

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.