2R8S | pdb_00002r8s

High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TZI	PDB ENTRY 1TZI 1HR2
experimental model	PDB	1HR2	PDB ENTRY 1TZI 1HR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	34% MPD, 0.1M sodium citrate, 0.2M ammonium acetate, 25 mM magnesium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.085	α = 90
b = 53.23	β = 108.42
c = 160.555	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	SBC-2	mirrors	2006-05-29	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-06-05	M	SINGLE WAVELENGTH
3	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-06-15	M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D
3	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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
1,2,3	1.95	20	98.6	0.088	16.7	5.2	77127	77127

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)
1,2,3	1.95	2		95.5	0.48	1.6	2.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TZI 1HR2	1.95	20	77127	77127	3875	98.6	0.19632	0.19632	0.19476	0.2	0.22607	0.23	RANDOM	35.918

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]
-2.23		-0.4	0.94		1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.954
r_dihedral_angle_4_deg	14.991
r_dihedral_angle_3_deg	14.124
r_dihedral_angle_1_deg	7.445
r_scangle_it	3.183
r_scbond_it	2.349
r_mcangle_it	2.092
r_angle_refined_deg	1.33
r_mcbond_it	1.271
r_angle_other_deg	1.022
r_mcbond_other	0.326
r_nbtor_refined	0.212
r_nbd_other	0.205
r_symmetry_vdw_other	0.183
r_nbd_refined	0.162
r_symmetry_vdw_refined	0.151
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.141
r_nbtor_other	0.08
r_chiral_restr	0.059
r_metal_ion_refined	0.038
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3263
Nucleic Acid Atoms	3404
Solvent Atoms	529
Heterogen Atoms	4

Software

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