4HVT | pdb_00004hvt

Structure of a Post-proline cleaving enzyme from Rickettsia typhi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		An initial model was obtained from iodide SAD phasing using crystal 2 (P21). The initial model was then used as search model for C2 high resolution data set, crystal 1.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	Microlyic MCSG1 screen b10: 24% PEG 4000, 20% Glycerol, 160mM Magnesium Chloride, 80mM Tris:HCl pH 8.5; RityA17583bB2.PS01616 at 26.6mg/ml, cryo: EG; SG C2; for phasing crystal 2 was used SG P21, VAPOR DIFFUSION, SITTING DROP, temperature 290K
2	VAPOR DIFFUSION, SITTING DROP	7.5	290	Microlyic MCSG1 screen c5: 20% PEG 3350, 200mM Magnesium acetate; RityA17583bB2.PS01616 at 26.6mg/ml, for phasing a crystal was soaked in reservoir + 20% EG with 2.5M sodium iodide (final 500mM NaI) for 1 minute, this sample is from a differet space group (P21) than crystal 1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.44	50
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.59	α = 90
b = 73.28	β = 98.52
c = 55.46	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	100	CCD	ADSC QUANTUM 315r		2012-10-14	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	RIGAKU SATURN 944+		2012-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.7	50	99	0.065	16.86	4.8	87031	86126		-3	23.221

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	1.7	1.74	98		0.493	3.42

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD, MOLECULAR REPLACEMENT	THROUGHOUT	An initial model was obtained from iodide SAD phasing using crystal 2 (P21). The initial model was then used as search model for C2 high resolution data set, crystal 1.	1.7	50	87031	81804	4322	98.97	0.1723	0.1723	0.1704	0.18	0.2093	0.21	RANDOM	19.2341

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]
0.14		0.54	0.79		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.673
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_4_deg	11.997
r_dihedral_angle_1_deg	6.687
r_angle_refined_deg	1.683
r_angle_other_deg	0.85
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5510
Nucleic Acid Atoms
Solvent Atoms	746
Heterogen Atoms	26

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction