7CX7 | pdb_00007cx7

Crystal structure of Arabinose isomerase from hybrid AI8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AJT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	35% (v/v) MPD, 100mM Imidazole/ Hydrochloric acid pH 8.0, 200mM Magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.591	α = 90
b = 81.907	β = 117.9
c = 192.001	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	193	PIXEL	DECTRIS PILATUS3 6M		2020-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 11C	0.97942	PAL/PLS	11C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.49	50	99.2	0.121	0.131	0.05	4	6.7		97080

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	99.5		0.851	0.924	0.356	0.722		6.6

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	2AJT	2.49	48.59	92249	4784	98.59	0.1957	0.192	0.1932	0.2677	0.2643	RANDOM	46.375

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]
0.05		0.03	-0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.157
r_dihedral_angle_4_deg	20.914
r_dihedral_angle_3_deg	17.243
r_dihedral_angle_1_deg	8.165
r_angle_refined_deg	1.54
r_angle_other_deg	1.286
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23440
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	87

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing