1V03 | pdb_00001v03

Crystal structure of the Sorghum bicolor dhurrinase 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E1E	PDB ENTRY 1E1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		2.0 M NH4(SO4)2, 0.1 M HEPERS PH 7.5, 50 MM NACL

Crystal Properties
Matthews coefficient	Solvent content
5.98	79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 195.49	α = 90
b = 195.49	β = 90
c = 195.49	γ = 90

Symmetry
Space Group	P 41 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2003-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		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	2	39	99.8	0.073	6.8	7.9		85811

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	2	2.07	99.7		0.328	2.2	7

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 1E1E	2	141.42	81445	4294	99.8	0.189	0.187	0.19	0.213	0.21	RANDOM	28.89

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.849
r_scangle_it	2.57
r_mcangle_it	2.332
r_scbond_it	1.702
r_angle_refined_deg	1.529
r_mcbond_it	1.422
r_symmetry_hbond_refined	0.253
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.205
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.112
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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	3898
Nucleic Acid Atoms
Solvent Atoms	600
Heterogen Atoms	22

Software

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