F-ACTIN IS A HELICAL POLYMER OF ACTIN MOLECULES. THE Z-AXIS OF THE ACTIN COORDINATES SHOWN IN THIS PDB-FILE IS A HELIX AXIS. THE NEXT SUBUNIT IN F-ACTIN IS POSITIONED BY 166.4 DEGREE RIGHT ROTATION ABOUT THE HELIX AXIS AND 27.59 ANGSTROM SHIFT ALONG THE HELIX AXIS.
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Components
#1: Protein
Actin, alphaskeletalmuscle / Alpha-actin-1
Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rabbit skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
Resolution: 3.3→56 Å / Rfactor all: 0.143 Details: THE DIFFRACTION DATA WERE EXTRACTED USING THE PROPER HELICAL SYMMETRY SUCH AS A SELECTION RULE L=-153N+331M AND A REPEAT DISTANCE 9135 ANGSTRUM. THE LAYER-LINE DISTRIBUTION BY THE SELECTOIN ...Details: THE DIFFRACTION DATA WERE EXTRACTED USING THE PROPER HELICAL SYMMETRY SUCH AS A SELECTION RULE L=-153N+331M AND A REPEAT DISTANCE 9135 ANGSTRUM. THE LAYER-LINE DISTRIBUTION BY THE SELECTOIN RULE IS CLOSE TO THAT BY L=-6N+13M IN PRINCILE ONE LAYER-LINE BY L=-6N+13M SEPARATES SEVERAL LAYER-LINES BY L=-153N+331M. BUT THE SEPARATIONS WERE NOT CLEAR AND THE LAYER-LINE INTENSITYIES WERE EXTRACTED AS "GROUPING LAYER-LINE INTENSITIES" FROM EXPERIMANTAL PATTERNS. THEN THE LAYER-LINE INTENSTITIES WERE HANDLED AS "GROUPING LAYER-LINE INTENSITIES" RE-INDEXED BY L=-6N+13M. THE INITIAL MODELS OF F-ACTIN WERE MADE FROM THE THREE CRYSTAL STRUCTURE OF 1J6Z, 2BTF AND 1HLU. FIRST THE RADIUS AND THREE ORIENTAIONS OF THE SUBUNIT IN F-ACTIN WERE DETERMINED BY THE RIGID BODY SEARCH USING THE DIFFRACTION DATA OF 56-7.2 ANGSTROM. NEXT THE SUBUNIT COMFORMATIONS WERE SEARCHED ALONG THE ADDITIONAL 12 LOWEST ELASTIC NORMAL MODES OF ACTIN MONOMER VIBRATIONS BY COMPARISON BETWEEN THE EXPERIMETAL DIFFRACTION DATA AND THE CALCULATION AT 56-7.2 ANGSTROM. THE DIFFRACTION WAS CALCULATED USING A REPEAT DISTANCE OF 9135A AND A SELECTION RULE L=-153N+331M. THE CALCULATED LAYER-LINE INTENSTITIES ALSO WERE HANDLED A "GROUPING LAYER-LINE INTENSITIES" RE-INDEXED BY L=- 6N+13M. WE CAN NOT FIND THE GOOD SOLVENT MODEL AROUND F-ACTIN. THEN WE USED TWO KINDS OF ATOMIC SCATTERING FACTORS AT THE HIGH RESOLUTION AND THE LOW RESOLUTION DATA.THE MOLECULAR DYNAMICS REFINEMENT AND ENERGY-MINIMIZATION WERE REPEATED IN TRUN USING THE LOW RESOLUTION DATA (RADIALLY 6.5-56 A FROM ORIGIN) AND THE HIGH RESOLUTION DATA (RADIALLY 3.3-5.5 A AND LATERALLY FROM THE MERIDIAN TO 5.5 A) BY FX-PLOR. TO JUDGE THE MODELS, TWO KINDS OF R-FACTORS WERE CALUCLATED AGAINT THE DIFFRACTION PATTERN TO AVOID THE DECOMVOLUTION ERROR. R-FACTOR-FIT IS AN R-FACTOR AGAINST FITTING AREA (THE AREA RADIAL 6.5-56 and 3.6-5.5A AND LATERALLY FROM THE MERIDIAN TO 5.8 A). THE R-FACTOR-NON-FIT IS AN R-FACTOR AGAINST NON-FITTING AREA (THE AREA RADIALLY 5.5 - 6.5 A AND LATERALLY TO 15 A). R-FACTOR-FIT : 0.143 R-FACTOR-NON-FIT : 0.207
Refinement step
Cycle: LAST / Resolution: 3.3→56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2933
0
28
0
2961
+
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