1OC7 | pdb_00001oc7

D405N mutant of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with methyl-tetrathio-alpha-d-cellopentoside at 1.1 angstrom resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OC5	PDB ENTRY 1OC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		PROTEIN WAS CONCENTRATED TO 20 MG/ML IN WATER. CRYSTALLISATION IN 100MM MAGNESIUM ACETATE, 100MM ACETATE BUFFER AT PH 4.6. PRECIPITANT WAS 21% POLYETHYLENE GLYCOL 5000MME AND 5% DIMETHYLFORMAMIDE AS ADDITIVE.THE PROTEIN WAS INCUBATED WITH 1MM OF THE INHIBITOR PRIOR CRYSTALLISATION FOR AT LEAST 1 HOUR.

Crystal Properties
Matthews coefficient	Solvent content
4.05	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.504	α = 90
b = 60.148	β = 90
c = 97.207	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	MARRESEARCH		1999-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	1.1	20	96	0.053	23.7	4.3		120133

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	1.1	1.13	91.5		0.242	5.6	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1OC5	1.11	20	120318	6359	94.5	0.106	0.105	0.13	0.124	0.14	RANDOM	8.57

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]
-0.31			0.28		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.071
r_dihedral_angle_4_deg	19.962
r_dihedral_angle_3_deg	10.94
r_dihedral_angle_1_deg	6.232
r_scangle_it	3.434
r_scbond_it	2.494
r_angle_refined_deg	1.907
r_angle_other_deg	1.861
r_mcangle_it	1.822
r_mcbond_it	1.269
r_nbd_other	0.274
r_symmetry_vdw_other	0.253
r_nbd_refined	0.234
r_symmetry_vdw_refined	0.163
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.122
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbtor_refined
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2839
Nucleic Acid Atoms
Solvent Atoms	603
Heterogen Atoms	98

Software

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