Experiment: 3ZP8

HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1.7M SODIUM MALONATE, PH 7.5 AND 1 MM MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.82	α = 90
b = 68.53	β = 112.35
c = 58.9	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	MARMOSAIC 325 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.55	20.39	97.6	0.03	13.9	3		26462			24.76

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	1.55	1.63	99.6		0.63		3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2GOZ	1.55	20.39	1.34	26446	2002	97.48	0.1889	0.1867	0.1888	0.2157	0.2162

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.414
f_angle_d	0.945
f_chiral_restr	0.041
f_plane_restr	0.008
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1344
Solvent Atoms	289
Heterogen Atoms	16

Software

Software
Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
PHENIX	phasing