4Y9M

PA3825-EAL Metal-Free-Apo Structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	277	0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic and 0.1 M sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.34	α = 90
b = 64.34	β = 90
c = 134	γ = 90

Symmetry
Space Group	P 43 21 2

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	DECTRIS PILATUS 6M		2014-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.6	64.34	99.9	0.064	18	9.3	40170	36008

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	1.642	99.9		0.601	3.2	9.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3N3T	1.6	58	36008	1886	99.76	0.18462	0.18243	0.22707	RANDOM	22.217

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]
-0.13			-0.13		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.949
r_dihedral_angle_4_deg	18.563
r_dihedral_angle_3_deg	11.199
r_long_range_B_refined	6.351
r_long_range_B_other	6.276
r_dihedral_angle_1_deg	5.157
r_scangle_other	4.519
r_scbond_other	3.043
r_scbond_it	3.04
r_mcangle_other	2.097
r_mcangle_it	2.095
r_angle_refined_deg	1.674
r_mcbond_it	1.471
r_mcbond_other	1.447
r_angle_other_deg	1.002
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1999
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing