3D7K | pdb_00003d7k

Crystal structure of benzaldehyde lyase in complex with the inhibitor MBP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AG0	PDB ENTRY 2AG0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.9	293	50% PEG 200, 100 mM MES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.936	α = 90
b = 151.936	β = 90
c = 98.217	γ = 120

Symmetry
Space Group	P 32 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 315		2006-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B		APS	14-ID-B

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	2.19	46	80.7	0.138	12.4	8		54267		3

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 (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 2AG0	2.49	46	54025	40253	4485	97.21	0.19977	0.19411	0.19	0.24958	0.25	RANDOM	50.501

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]
0.7	0.35		0.7		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.956
r_dihedral_angle_3_deg	18.478
r_dihedral_angle_4_deg	16.138
r_dihedral_angle_1_deg	6.848
r_scangle_it	3.612
r_scbond_it	2.398
r_angle_refined_deg	1.916
r_mcangle_it	1.597
r_mcbond_it	0.935
r_nbtor_refined	0.316
r_nbd_refined	0.239
r_metal_ion_refined	0.236
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.205
r_xyhbond_nbd_refined	0.184
r_chiral_restr	0.123
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8158
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing