2C46 | pdb_00002c46

CRYSTAL STRUCTURE OF THE HUMAN RNA guanylyltransferase and 5'- phosphatase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I9S	PDB ENTRY 1I9S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				2 M POTASSIUM CITRATE

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.4	α = 90
b = 161.6	β = 104.7
c = 60.7	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	CCD	MARRESEARCH	MIRRORS	2005-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.6	47.9	90.4	0.08	10.29	3.79		133485		3

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	1.6	1.7	87.9		0.4	2.71	2.73

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 1I9S	1.6	80.85	126725	6714	90.4	0.206	0.204	0.2	0.234	0.21	RANDOM	28.35

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]
0.3		-0.12	0.82		-1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.784
r_dihedral_angle_3_deg	14.109
r_dihedral_angle_4_deg	10.792
r_dihedral_angle_1_deg	5.876
r_scangle_it	2.421
r_scbond_it	1.612
r_angle_refined_deg	1.342
r_mcangle_it	1.083
r_angle_other_deg	0.892
r_mcbond_it	0.702
r_symmetry_vdw_other	0.266
r_nbd_refined	0.204
r_nbd_other	0.179
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.134
r_symmetry_vdw_refined	0.107
r_chiral_restr	0.102
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
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	6215
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing