1GYH | pdb_00001gyh

Structure of D158A Cellvibrio cellulosa alpha-L-arabinanase mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		MAP FROM AN A P6522 CRYSTAL FORM SOLVED BY MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		18% PEG5000 MME, 4% AMMONIUM SULFATE, 100MM NA-CACODYLATE PH6.5, 20% GLYCEROL, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.556	α = 88.83
b = 79.557	β = 89.58
c = 132.402	γ = 83.58

Symmetry
Space Group	P 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 CCD			M	SINGLE WAVELENGTH

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

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	1.9	20	97.4	0.066	12.37	1.89		155379

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	1.9	1.94	89.8		0.269	3.08	1.75

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MAP FROM AN A P6522 CRYSTAL FORM SOLVED BY MAD	1.89	20	154093	730	96.6	0.147	0.147	0.23	0.203	RANDOM	14.75

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]
0.12	0.44	-0.34	-1.25	0.48	1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.002
r_scangle_it	4.089
r_scbond_it	2.929
r_mcangle_it	1.899
r_angle_refined_deg	1.517
r_angle_other_deg	1.484
r_mcbond_it	1.311
r_symmetry_vdw_other	0.308
r_nbd_other	0.257
r_symmetry_hbond_refined	0.193
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.186
r_symmetry_vdw_refined	0.123
r_chiral_restr	0.104
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
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	15319
Nucleic Acid Atoms
Solvent Atoms	1910
Heterogen Atoms	6

Software

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