2BWN | pdb_00002bwn

5-Aminolevulinate Synthase from Rhodobacter capsulatus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BS0	PDB ENTRIES 1BS0 AND 1FC4
experimental model	PDB	1FC4	PDB ENTRIES 1BS0 AND 1FC4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		100 MM HEPES, PH 7.5, 200 MM NA ACETATE, 8% (V/V) ISOPROPANOL, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.875	α = 90
b = 92.872	β = 90
c = 250.131	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	CCD	MARRESEARCH	MIRRORS	2003-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	2.1	50	83.8	0.08	13.7	4.7		370565

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	2.1	2.18	82.7		0.34	3.8	4.7

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 ENTRIES 1BS0 AND 1FC4	2.1	129.1	74301	3874	83.7	0.164	0.161	0.17	0.217	0.23	RANDOM	18.95

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]
-1.75			0.49		1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.661
r_dihedral_angle_4_deg	17.682
r_dihedral_angle_3_deg	15.095
r_dihedral_angle_1_deg	4.465
r_scangle_it	4.132
r_mcangle_it	3.21
r_scbond_it	3.044
r_mcbond_it	2.826
r_angle_refined_deg	1.693
r_angle_other_deg	1.17
r_mcbond_other	0.566
r_symmetry_vdw_other	0.219
r_nbd_refined	0.194
r_nbd_other	0.172
r_nbtor_refined	0.167
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.151
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.124
r_nbtor_other	0.083
r_xyhbond_nbd_other	0.048
r_bond_refined_d	0.021
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	12132
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	102

Software

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