4MLV

Crystal Structure of Bacillus megaterium porphobilinogen deaminase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1M sodium cacodylate, 0.2M magnesium acetate, 25-30% PEG 8K, pH 6.5 - 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.32	α = 90
b = 65.78	β = 90
c = 97.21	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	PIXEL	PSI PILATUS 6M		2013-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.455	48.6	100	0.061	14.4	6.2	60772	60772

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	1.455	1.53	100		0.559	3	6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PDA	1.455	46.75	60772	57626	3073	99.98	0.14331	0.14112	0.18559	RANDOM	23.972

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]
			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.127
r_sphericity_free	25.619
r_dihedral_angle_4_deg	22.985
r_dihedral_angle_3_deg	13.854
r_sphericity_bonded	11.816
r_rigid_bond_restr	8.154
r_dihedral_angle_1_deg	6.369
r_scbond_other	5.689
r_scbond_it	5.685
r_scangle_other	5.589
r_long_range_B_refined	4.98
r_long_range_B_other	4.808
r_mcangle_other	3.331
r_mcangle_it	3.325
r_mcbond_it	2.796
r_mcbond_other	2.734
r_angle_refined_deg	2.438
r_angle_other_deg	2.208
r_chiral_restr	0.158
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2253
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	65

Software

Software
Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling