1Z3T

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

X-RAY DIFFRACTION

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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
2.2	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.414	α = 90
b = 46.842	β = 102.99
c = 99.488	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		1999-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9370	ESRF	ID14-4

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	50	99.6	0.098	11	4.3	43328	43328

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	1.73	93.1		0.321	5.8		2867

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1GPI	1.7	40	40782	40782	2541	100	0.172	0.16125	0.15879	0.19866	RANDOM	20.816

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]
2.53		-0.74	-1.17		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.152
r_sphericity_free	6.634
r_scangle_it	6.12
r_dihedral_angle_1_deg	5.299
r_sphericity_bonded	4.677
r_scbond_it	4.357
r_mcangle_it	3.204
r_rigid_bond_restr	2.599
r_mcbond_it	2.125
r_angle_refined_deg	2.062
r_angle_other_deg	0.983
r_nbtor_other	0.694
r_symmetry_hbond_refined	0.606
r_xyhbond_nbd_refined	0.362
r_symmetry_vdw_refined	0.357
r_nbd_refined	0.35
r_symmetry_vdw_other	0.301
r_nbd_other	0.211
r_chiral_restr	0.135
r_xyhbond_nbd_other	0.053
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3198
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	37

Software

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