2VBD | pdb_00002vbd

Isopenicillin N synthase with substrate analogue L,L,L-ACOMP (unexposed)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BK0	PDB ENTRY 1BK0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML TRIPEPTIDE, 25MG/ML IPNS

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.537	α = 90
b = 71.314	β = 90
c = 100.651	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	MIRRORS	2005-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	1.99	18.17	97.7	0.09	19.5	6.6		23160			17.57

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	1.99	2.1	85.9		0.27	7.4	6.1

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BK0	2	58.22	22198	909	99	0.169	0.167	0.17	0.216	0.22	RANDOM	11.76

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]
-0.35			0.63		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.496
r_dihedral_angle_3_deg	13.755
r_dihedral_angle_4_deg	8.975
r_dihedral_angle_1_deg	6.752
r_scangle_it	4.281
r_scbond_it	3.095
r_angle_refined_deg	1.798
r_mcangle_it	1.728
r_mcbond_it	1.41
r_angle_other_deg	1.097
r_symmetry_vdw_other	0.253
r_nbd_refined	0.219
r_nbd_other	0.195
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.157
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.116
r_symmetry_hbond_refined	0.112
r_nbtor_other	0.09
r_bond_refined_d	0.024
r_bond_other_d	0.012
r_gen_planes_refined	0.009
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	2645
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing