8AH9 | pdb_00008ah9

De novo retro-aldolase RAbetaB-16.1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	2 M ammonium sulfate, 0.1 M Bis-TRIS, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.482	α = 90
b = 77.485	β = 90
c = 60.652	γ = 90

Symmetry
Space Group	C 2 2 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	DECTRIS PILATUS 2M-F		2021-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.737	45.11	99.96	0.024	0.034	0.024	0.999	17.82	2		13587			24.72

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81			0.565	0.565

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6czg,6czj, 6d0t	1.747	45.11	13587	677	99.904	0.188	0.1865	0.2	0.2257	0.22	29.35

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]
0.287			0.341		-0.629

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.403
r_dihedral_angle_3_deg	13.93
r_dihedral_angle_2_deg	13.38
r_lrange_it	11.631
r_lrange_other	11.625
r_scangle_it	9.265
r_scangle_other	9.26
r_dihedral_angle_1_deg	5.988
r_scbond_it	5.683
r_scbond_other	5.678
r_mcangle_it	3.453
r_mcangle_other	3.453
r_mcbond_it	2.663
r_mcbond_other	2.272
r_angle_refined_deg	1.487
r_angle_other_deg	0.493
r_xyhbond_nbd_refined	0.303
r_nbd_refined	0.204
r_symmetry_nbd_other	0.203
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.184
r_nbd_other	0.159
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	925
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing