1QMH | pdb_00001qmh

Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QMI	PDB ENTRY 1QMI, CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.

Crystal Properties
Matthews coefficient	Solvent content
2.84	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.8	α = 90
b = 133.5	β = 90
c = 51	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	IMAGE PLATE	MARRESEARCH		1998-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B		NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	20	97.2	0.043	11.3	3.2		50057		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.17	83.4		0.268	3.6	2.8

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 1QMI, CHAIN A	2.1	10	48203	2286	93.6	0.207	0.204	0.18	0.276	0.24	RANDOM	37.1

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
p_transverse_tor	21.1
p_staggered_tor	17.5
p_scangle_it	4.6
p_planar_tor	4.3
p_mcangle_it	3.8
p_scbond_it	3
p_mcbond_it	2.6
p_multtor_nbd	0.261
p_singtor_nbd	0.196
p_chiral_restr	0.185
p_xyhbond_nbd	0.171
p_planar_d	0.056
p_angle_d	0.046
p_plane_restr	0.029
p_bond_d	0.022
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4971
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	35

Software

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