1W2Z | pdb_00001w2z

PSAO and Xenon

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	HANGING DROP VAPOR DIFFUSION AT 293K. RESERVOIR WAS 20% PEG 3350, 0.28M KI. DROPS WERE 2 MICROL OF PSAO AT 21.58MG/ML IN 0.1M KPO4 PH 7.2, PLUS 1 MICROL OF 0.1M KPO4 PH 7.5, PLUS 1 MICROL OF RESERVOIR SOLUTION. THE CRYSTAL WAS CRYOPROTECTED BY SOAKING FOR 5 MIN IN 5 MICROL OF 0.2M KI, 25% PEG 3350 AND 15% GLYCEROL UNDER 30MICROL OF PARAFFIN IN A SITTING DROP DEPRESSION. THE CRYSTAL WAS EXPOSED TO XENON GAS FOR 5 MINUTES, INITIALLY AT PRESSURE OF 100 PSI THEN INCREASING TO A FINAL PRESSURE OF 220 PSI, USING A XENON CHAMBER (HAMPTON RESEARCH). AFTER THE XENON WAS RELEASED FROM THE CHAMBER, THE CRYSTAL WAS SNAP-FROZEN IN LIQUID NITROGEN WITHIN 1-3 S.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.507	α = 90
b = 196.268	β = 107.46
c = 89.665	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	OSMIC MIRROR	2004-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.24	29.82	99.8	0.07	17	4.75		141039		-3	28.5

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	2.24	2.3	98.9		0.17	7.7	4.7

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	PDB ENTRY 1KSI	2.24	29.88	133957	7082	99.8	0.181	0.179	0.19	0.224	0.23	RANDOM	19.5

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]
-0.52		-1.02	0.06		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.218
r_scangle_it	5.974
r_scbond_it	4.158
r_mcangle_it	2.698
r_mcbond_it	1.539
r_angle_refined_deg	1.322
r_angle_other_deg	0.806
r_nbd_other	0.236
r_symmetry_vdw_other	0.222
r_symmetry_vdw_refined	0.202
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.083
r_nbtor_other	0.082
r_bond_refined_d	0.012
r_metal_ion_refined	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20648
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	304

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing