2IUO | pdb_00002iuo

Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DW9	PDB ENTRY 1DW9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3		CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3.

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.6	α = 70.02
b = 80.75	β = 71.81
c = 82.28	γ = 66.34

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	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	1.85	40	92.5	0.05	14	2.2		129043

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	1.85	1.92	59.9		0.24	2.5	2.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1DW9	1.9	76.7	117862	6261	94.8	0.152	0.149	0.208	RANDOM	13.54

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]
0.77	0.86	-1.52	-0.68	-0.1	0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.122
r_dihedral_angle_3_deg	13.748
r_dihedral_angle_4_deg	10.487
r_dihedral_angle_1_deg	6.415
r_scangle_it	3.818
r_scbond_it	2.941
r_angle_refined_deg	1.845
r_mcangle_it	1.509
r_mcbond_it	1.342
r_angle_other_deg	1.079
r_nbd_refined	0.24
r_symmetry_hbond_refined	0.228
r_nbd_other	0.213
r_xyhbond_nbd_refined	0.199
r_symmetry_vdw_other	0.188
r_nbtor_refined	0.173
r_chiral_restr	0.116
r_symmetry_vdw_refined	0.111
r_nbtor_other	0.087
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	11960
Nucleic Acid Atoms
Solvent Atoms	2052
Heterogen Atoms	138

Software

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