4MLQ

Crystal structure of Bacillus megaterium porphobilinogen deaminase

X-RAY DIFFRACTION

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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
2.42	49.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.01	α = 90
b = 65.12	β = 90
c = 96.78	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	MARMOSAIC 225 mm CCD		2013-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	1.072	ESRF	BM14

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	1.6	31.33	95.6	0.088	10.1	6.4	42866	42866

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	1.6	1.69	88.7		1.493	0.9	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	31.33	42728	40552	2176	95.05	0.16462	0.16061	0.24215	RANDOM	28.019

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]
-0.16			0.47		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.063
r_dihedral_angle_2_deg	35.539
r_dihedral_angle_4_deg	22.7
r_sphericity_bonded	19.976
r_dihedral_angle_3_deg	15.1
r_scangle_other	8.648
r_long_range_B_refined	8.563
r_long_range_B_other	8.56
r_scbond_it	7.874
r_scbond_other	7.871
r_mcangle_other	6.968
r_mcangle_it	6.947
r_dihedral_angle_1_deg	6.18
r_mcbond_it	5.839
r_mcbond_other	5.828
r_rigid_bond_restr	5.224
r_angle_refined_deg	2.142
r_angle_other_deg	1.526
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.004
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	2245
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	65

Software

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